The sorts of changes that aren't adding units/wonders (or if so, are only minimalistically so and logically done), and which don't extensively modify things, but which do provide some change.
I don't particularly enjoy some scenarios as much as others and I don't think modifying them would fix that.
I don't really enjoy the WWII scenario and no modification will change it.
I enjoy the stuff in the Mesoamerican scenario, but playing it once kills all feeling of need to play it again. Also, its unique features are easily imported into the Age of Discovery scenario.
I enjoy the Sengoku/Shogun scenario, but playing it once kills all feeling of need to play it again especially once you learn that literally the only difference between the civs is their starting location; the only difference in playthroughs is in which method of winning you decide to pursue. (War Council is ridiculously easy to get elected to if you can manage to keep the island nations stuck on being islands and literally control the entirety of the mainland via having wiped out altogether all mainland nations.)
I enjoy the Mesopotamian scenario, but as-is the only changes I'd make are to the VP limit (it needs to be like, double, because it's too easy to achieve) and the time limit (it could use being longer). Maybe retaining culture of cities captured but that's a feature I love regardless of scenario anyway.
Rise of Rome I've modded already, multiple times in fact, it being my favorite scenario and all that, so I wouldn't be doing it again.
Which leaves Fall of Rome, The Middle Ages, Age of Discovery, and Napoleonic Europe.
Napoleonic Europe, I'd make one change only; the ability to culturally convert cities (seriously why the heck is that option ever off?), which would make Espionage actually be useful. (What's the point of it if not to use Propaganda? Troop movement is useless because on any computer due to whatever coding went into the system, civ 3 can only show so many units moving even with animations disabled before you get the laggy wheel of doom that causes you to miss what said units are doing. It also only lasts one turn and is redundant since just HAVING a spy tells you troop amounts and if you know how many troops they have you can deduce said troops' locations fairly easily. World map's worthless especially on a map you have fully revealed. Tech? You can do that without a spy. Investigating a city? You can do that without a spy. Sabotaging production? In a scenario with no wonders to build, worthless.)
Okay maybe I'd make it so that other cavalry units than the Cossack have Blitz? Because Russia's ability to Blitz with Cossacks makes nobody else worth playing.
Maybe I'd eliminate the war weariness that's annoying for playing as France? You're literally LOCKED IN A WAR YOU CAN'T MAKE PEACE IN and have to deal with war weariness as a result, not to mention the invisible warmongery penalties that I know exist but don't know the exact mechanics of because I don't particularly care to. (Butstill, are bs because you can incur severe warmongry penalties for a war you didn't even start.)
Very small, minute changes to make the scenario something more fun to play in. Still wouldn't play as anyone other than Russia or France (France has the best units stat-wise bar none and starts with three armies, so if you're in any way shape or form aggressive you can conquer the world ridiculously easily, it's just a matter of being aggressive to surpass the city advantage Russia starts with), but it'd make the scenario be more replayable to me.
For Age of Discovery, I'd retain culture on capture of cities--given that it's almost impossible for me to win by culture (I've tried with the Mayans who're best suited for it and while I came close, didn't manage it), it'd be tempting to leave that variable unchanged, but I recognize that I would need to adjust it somewhat. Not a full double, but maybe like 1.5x as much.
I'd definitely double the amount of turns in the game, though, because seriously, even if you go 100% science the entire game (only possible on Chieftain difficulty, mind you, as the easiest difficulty's the only one where you're not penalized for having no treasury), you can't actually research all tech. (Dropping the minimum turn number for techs from 4 to 2 would help there, too.)
Victory Points is difficult to do as well; as Portugal literally wiping out everyone except the Spanish to have complete control of the map and limiting the Spaniards to Cagliari (basically, preventing them from EVER settling anywhere else if you put so much as a caravel in the straights of Gibraltar), building every single wonder, and having as many units transporting treasure as I could get, I only barely pulled it off.
So like culture, I'd probably give it an increase, not full double but like 1.75x as much.
I'd make a lot of other changes, too, though.
I've tested the Mayans; there is literally no reason to go for the Mesoamerican civs. Even if you maintain a stranglehold on all of America (difficult, but possible, to do) and all of its surrounding landmasses, even if you have 100% science going the entire time...you can't out-compete with the European civilizations. Sure, you can eventually match their tech level, but you can never surpass them. You run out of time before it's possible.
It's also impossible to out-European the European civs, meaning the only way to get all of those wonders they complete first would be to launch an invasion of Europe.
I can't fix that, but I can mitigate it. My plan for that would be to give the Mesoamericans entire upgrade paths for units that all have the Enslave ability. A Mesoamerican Pikeman with Enslave; a Mesoamerican Longbowman with Enslave; a Mesoamerican Medieval Infantry with Enslave; a Mesoamerican Musketman with Enslave.
I would, in addition to making those units, make them cheaper than their European equivalents shield-wise to make.
This would give an actual incentive for me to play them; it would make them more unique and give them more of the vibe they are meant to give off. Sure, they would still lose the tech race and not have the European wonders, but this ability to have units that're cheaper, just as effective, and yet have Enslave, compared to their European versions? Worth. it.
Also I'd give them some of the Mesoamerican buildings as well, fit into their tech tree path.
I wouldn't just modify the Mesoamerican civs, though.
Currently, you have literally zero incentive to ever play as a Protestant Monarchy. Why? Because Jesuit Colleges are just too gamebreakingly powerful. Missionaries mass-produced, and boosting your scientific output? Not something you want to miss out on. So even if the theme were lost, I'd make them available to all governments.
Yes, this would mean less reason to play a Catholic Monarchy, but there are reasons to have the Catholic Monarchy even beyond their Jesuit College. The two governments are basically equals in terms of value without taking into effect their buildings/wonders; with said buildings/wonders, you'd never have reason to go Non-Catholic.
I might modify the Missionary unit, make it nationless and maybe not require upkeep (they are, after all, mass-produced!), but most of my modifications would in fact be to make Portugal not be the only viable player nation.
England's Sea Dogs would become nationless, because seriously them not having a nationless sea unit kinda defeats the point of producing that line of unit in the first place. I'd probably also give them the Ship-of-the-Line unit so that they have unquestioned dominance over naval sea power, their intended specialty.
Amsterdam I'd buff their Swiss Mercenaries and reduce their shield cost as to make them viable.
France, I'd make their Musketeers be much, much cheaper.
And similarly, Spain's Conquistadors? Why the heck is a 3/2 unit cost 70 shields when it is replacing a unit costing 20? Why the heck is a 3/2 unit with amphibious assault costing 70 shields when the other amphibious assault units cost 30/40 shields and have stronger attack/defense (respectively)? I'd half its build cost as a result, to be ~35ish.
Would this perfectly balance things out? No, but it'd make it more equal all-around, because as-is, really. You just never have any reason to ever play anyone other than Portugal. They're just...the best all-around as-is. They can conquer Europe and conquer the New World without really breaking a sweat. In spite of having no unique unit, what they are given is just...it's enough where it's basically impossible for them to lose if you're playing even remotely competently/aggressively.
Since that's a lot of changes to Age of Discovery, probably not the one I'd work on.
But there's still Fall of Rome and The Middle Ages.
For Fall of Rome, what I'd basically do is "do what I did before, but properly rather than messily".
Give the Sassanids the entry tech on the Barbarian tech tree but compensate the other Barbarian nations by giving them the first three levels in it. Nerf Legionary defense by one. Increase Horseman/Heavy Cavalry/Raider/Marauder/Pillager/Warlord movement by one. Make Warlords cheaper than Heavy Cavalry, and create Pillagers instead of Marauders. (Because you have incentive to keep Pillagers as they create Workers themselves.)
A few wonder tweaks/additions.
Sassanids starting with a couple extra Heavy Cavalry and an Army because I don't want to bother with the save scumming necessary to create one every single game (which I did on every single one of my Sassanid playthroughs, save scummed until one of your starting two "Immortals" heavy cavalries produced a leader).
Change the city elimination to be 10 instead of 8. (Frankly I'd like it if I could set that at 12, but the max is 10.)
Frikkin' fix the land bridge for Constantinople so I don't have to travel half way across the map in order to take the city, a feature unique to this scenario only (as literally every other scenario with that location has there be a land bridge--Mesopotamia, Rise of Rome, The Middle Ages, and Napoleonic Era all have it be land, not sea).
Double the needed VP points to win and increase (but not double) the number of turns in the game.
Small stuff, but which I messed up the first time. (I set the VP points way too high, for instance, and literally doubled the turns which is tortuously long, making the scenario nigh-unwinnable except with an insane amount of time spent.)
And then there's the Middle Ages scenario, which I wouldn't need to add a thing to, just tweaking existing things as to make it be less annoying.
I'd have the Christian civilizations start with the first three in their tech tree, to make it harder to out-Christian the Christian civilizations. (Harder, but not impossible.) Because I can easily build the Holy Roman Empire as the Kievan Rus, Turks, Abbasids, and so on and so forth. You just have to focus on it the second you can, and if you complete it, magically, you get two bonus techs; if you were in any way behind because of focusing on the wrong tech tree, those two techs boost you up and mean you lose nothing.
I'd rework all the cavalry units. I'd make the Sipahi have three movement and gain blitz, make the Ansar Warrior have four movement, buff cataphracts' defense, and buff knights' attack, or something like that. Not sure the exact tweak I'd make, but I'd do something to make each of the four cavalry units be different from the other and the difference be something that makes them not be inferior, because as-is, you never have reason to use anything other than the Sipahi or the Ansar Warrior. Sipahi for being the best in attack; Ansar Warrior for being the best in movement.
I'd probably buff the berserk as well in some fashion.
I'd make the Kievan Rus be able to build both Longships and Dromons rather than just one, doing whatever would be necessary for that.
I'd make the pure Viking civilizations start with three of their techs, and have the three Caliphates start with three levels of their Arab techs. The Byzantines would also have three Byzantine techs. The Kievan Rus would start with both the first Viking tech and the first Byzantine tech (because seriously, it says that they favor the Byzantine tech tree but they start with nothing in it so that's an outright lie pretty much), with the Turks having the second Arab tech.
Beyond that, it'd just be a matter of unit tweaks. Specifically, making swordsmen upgrade into medieval infantry (who I'd add amphibious assault to) upgrade into crusaders (who'd gain the amphibious assault ability as well).
From there, all I'd need is minor building tweaks. Hospitals for city size 3 instead of 2, because screw only coastal cities being possible to get metropolises. A building being repurposed to include pollution reduction. Small tweaks to buildings, mostly in their cost, to match their more cheaper build costs. Maybe minor tweaks to wonders, but nothing that unusual.
Stuff that takes less than a day's work, I'd guess.
But who knows if I'll follow through, the idea sounds more and more boring and tedious the more I outline it.
If for no other reason than I still don't know how to get scores for custom scenarios recorded and these modified scenarios count as custom scenarios. A feeling of "what's the point" exists, more or less.