For machines, the answer is obvious--they are mass-produced, thus, why they are identical.
For non-humans (e.g. monsters), the answer is that they are different...but the differences are invisible to the naked human eye. Think like how many birds have plumes which to us humans look white and yet are actually vibrant colors to the birds themselves.
For humans, the answer is just to have every non-unique (i.e., repeatable) random encounter enemy be wearing a uniform, such that it is...well...uniform. Thus, while they all appear to be the same, they are actually different individuals. Just you can't tell the difference because they all look the same.
For all of the above, heroes are not mass-murderers, and thus, often, the foes are just knocked out. When the force used is explicitly lethal, this isn't actually that big a deal--because revival methods are commonplace in the setting, and thus, while they "kill" enemies they fight, allies of the enemies just revive them at a later time. (Does this explanation perfectly fit? I imagine not! But it gets closer than most RPGs to justifying having unlimited encounters.)
For summon-like enemies, the answer is obvious; summons wouldn't actually be permanently killable and would just be de-summoned when defeated.
For Nilrealm residents (who make up 40-50% of the game's total enemies), they exist outside the boundaries of time and space: they do not experience aging as we know it (though they do have a concept of stronger than before more or less, thus justifying palette swaps which're stronger versions of prior monsters), and cannot truly die as we know death.
As a result, when you 'kill' them, you don't permanently kill them. Furthermore, you can encounter multiple of the same enemy in a battle and have it be an identical enemy because thanks to existing outside the boundaries of space and time they can exist in the same spot in space/time as multiple selves.
This pretty much covers all the fights I can think of in terms of justifying how they all look identical. Something almost no other RPG does. (There are a few, but they are far and few between.)
Another thing I did was extrapolate on something I had already decided was a part of the game.
I had in mind that two characters had a sidequest where upon the conclusion of said sidequest, they would get married. As a consequence of this, they would receive the item, 'Wedding Ring', and only those two characters could equip those two rings.
I had already established that those two characters with said Wedding Rings would have no Ultimate Weapon/Armor because their rings would be a substitute FOR said ultimates. This is because the Wedding Ring, as I envisioned it, granted permanent immunity to ALL negative status ailments...and when both wedding rings are in the same party, granting ALL positive status effects at the time of entry into battle together. (In short, the characters get a bonus for fighting together.)
...Yet I further gave the wedding rings not one but TWO hidden attributes:
A hidden +1 to every stat per in-game hour the rings worn, with these stats doubled if both wedding rings are in the same party.
...And per game, this bonus would be doubled. As in, say you had played 50 hours with the rings on. +50, situationally +100. A NG+ would then grant +100, situationally +200. A third new game would grant +200, situationally +400. And so on and so forth.
Stats aside from HP/MP have an arbitrary cap at either 99 or 999. (The latter probably makes more sense.)
This hidden attribute bonus would allow the characters to exceed that arbitrary cap, to go as far as the game engine would let their stats be raised without it looping back. Essentially making them potentially nigh-infinite in strength compared to other characters. Provided you have the wedding rings equipped and keep playing for hours to grind them up. (One or two hours, not much of a difference. Twenty hours...)
In short, a grinder's best friend and ultimate reward. Something which tells them that, yes, their endless number of hours spent playing is not useless, and does serve a purpose.
...This, I already did before, though I don't think I blogged about it.
What I didn't do is assign these to characters.
Tentatively, today I have.
One is a character I already mentioned: the Darkness Archer. His backstory involves him coming from the Darkrealm, and more specifically, from a location where hunting with bows is a way of life both because of a need to survive that way and because of the culture. He's a hunter by trade, and has been for most of his life; comparatively speaking, he's a newbie at the whole 'hero' thing.
The love interest for him during the romance sidequest I decided would be a Beastmaster. What else she would be, haven't ironed that out yet (I will eventually), but that's her main class aesthetic. Her backstory is that she owns an animal shelter/farm of sorts. She is highly, highly empathetic, a bit naive, highly trusting in others, all-loving and the like. Sweet, innocent, caring, loving, has respect for all life, the works.
During the romance sidequest, I decided that there would be multiple options available.
Which options are selected would influence the ending of the game. As long as you try to encourage the romance, it will continue the sidequest. Or rather, as long as you don't actively discourage the romance, it will continue the sidequest. (As in, you deliberately have to go out of your way to make the romance fail. In short, you have to be a poisonous friend telling them to not interact with one another in order to make the sidequest not continue.)
One route is the "canonical" route, the route where there is the greatest level of love and understanding between the two at every turn, where they do everything right.
At the other extreme, there's an ending which has a different message, more or less that love can come in many different forms, that even when two people are so different and have all these numerous debilitating quirks, that if they can still put up with one another when both are at their worst in the worst of situations, that their love will still carry through, more or less.
There are many different variations which are somewhere between the two, depending on your advice to the happy, romantic couple. As long as they end up marrying one another, the (absolute) perfect ending is possible. And as with the case of a character leaving (as mentioned before), the game would actively warn you every step of the way if you were taking the choice which would sabotage the relationship.
I think that this would best be explained with an example. For instance, when the Darkness Archer comes to the protagonist for help in courtship advice (he wants to formally start dating her), the following are options available.
Ask her to show you how to take care of animals.
This is the "canonical" route, the one the game considers 'most right'. It triggers a loving, affectionate scene where the Beastmaster tries to show the Darkness Archer the ropes in taking care of the animals. It includes a few funny moments here and there as disaster is narrowly averted, but by and large is a bonding moment, where they spend intimate time together getting to better know one another, a real "D'awwwwwwwwwww" moment.
Don't show her any affection (WARNING: THIS OPTION WILL LOCK YOU OUT OF THE PERFECT ENDING).
If you select this, as before, there are four or five warning screens, each which by default will take you back to the menu. To go through with this, you have to really mean it. But if you're stupid/cruel enough to select this option, then more or less, he just goes, "...Oh." And does nothing. He walks off, and you never hear of the romance again, until the ending of the game where both characters lament their regrets.
Volunteer to take care of the animals.
This option triggers a rather humorous scene, still loving, but not quite as affectionate and bonding, in that the Dark Archer will offer to look after the animals for a time while she goes out and has fun--she accepts, not even thinking about whether he's qualified for the task or not. In short, because she's too trusting and a bit naive, she doesn't think about how much of a good idea it'd be, she just thinks it's sweet of him to offer and takes what was given to her.
Hilarity ensues, as the poor guy's well over his head. By the time she comes back, he is left in tears, bawling, both because of the NUMEROUS injuries he has sustained trying and epically failing at his task, and because of how trashed the place is thanks to his incompetence in having managed it. It's still a sweet moment, but more funny than anything else.
...And then, there is the option which is so tremendously stupid that you'd THINK it'd lock you out of the (Absolute) Perfect Ending...except it doesn't; you can still obtain that ending even when selecting what by all rights should be classified as sabotaging the relationship:
Present Boar's Head as Proof of Manhood.
This is a scene which I've considered making a comic of all day because words just wouldn't do it justice.
Highlights include: her screaming, her fainting, the guys (that being, the protagonist and would-be-lover) freaking out about her having fainted, the protagonist cluelessly (rather than knowingly) asking, "I wonder why she had that reaction", and the Darkness Archer equally as cluelessly asking, hopefully,
"...Do you think she liked it?"
This is the option you need to select in order for her at the ending of the game to be like, "Why did I fall in love with an absolute idiot?", lamenting she married an absolute moron, because by that point to earn said ending presenting the boar's head as proof of manhood is the least of his antics. (This would be the "love can come in many ways" ending.)
It is absolutely meant to be the option you do not select in the game, but is available to those who want it.
If you're wondering why this option doesn't count as relationship sabotage, it's because Men Are Morons. Love Makes You Dumb. And the girl is smart, sweet, and empathetic enough to recognize this. When she recovers from her catatonic state, she makes it known that while she was mortified, she understood the intention behind the gift, even if she would prefer he have done something else (the game's way of hinting at you "pick a different option next time ya moron").
So that's what I worked on today.
I hope that you can get as much of a laugh out of this even without knowing the characters/scene as well as I do.