If a palette swap is used to distinguish elemental differences (for slimes/dragons/spirits etc.), or certain kinds of strong enemies(early bosses reappearing later with modified stats and a different color scheme), I don't really mind as they are technically different enemies.
I do however, hate it when there are a ton of enemies (and I do mean a ton) that share different names/stats/sizes but have the same moveset and look entirely the same (ie. Neptunia series) or are overdone in general to compensate for the lack of enemy types. (ie. Atelier series)
Especially for old-school games, palette swaps aren't the worst. The way I'd use them, one could convey what the monster's general species does, but also keep the players on their toes for new tricks that sub-breed might have.
For instance, one could give all goblins a trip attack. But a blue goblin could be an "imp" that has debuff magic, and a dark purple one could be a "bogeyman" with a high evasion rate; another still could be a green "gremlin" that can steal minor consumables. All different from garden variety, red-garbed goblins. Heck, maybe the red one could be a "redcap" with a HP drain skill?
Of note I like that older Dragon Quest games do palette swaps, but sometimes exclude elements from its variants. The knights from DQ1 sometimes don't have axes, for instance.
Its been done a lot and its done now i mean, Pokemon has their elemental monkeys, Monster Hunter has their "subspecies", Dragon Quest, Final fantasy, Breath of Fire...
Its a trope of its own and its done for many reasons, either save asset development, punch the player for thinking a metal slime would be the same as a normal slime, make "rare" versions of the enemies for achievement hunting/completionist purposes.
Everyone has their reason but its something anyone who has played an RPG is used to, and i have yet to see it really dreaded as a practice, unless you make a game with 50 monsters who are really 5 bases with 10 color swaps each thats just lazy design.
You can also make game mascosts with it as with my favorite example of "elemental variations":
To me this is one of those necessary evils if you don't have a big budget. I don't personally mind it as long as there's enough variation in enemies as it is, and if the palette swaps aren't just the same enemy but marginally stronger. (Aka. they have new moves and so on)
The game with my favorite approach to palette swaps definitely has to be Dark Chronicle (Dark Cloud 2), though. While they didn't necessarily change up the basic attacks for the enemies, the palette swaps tended to be complete overhauls of an enemy's core design complete with new texturing and so on. Like compare this guy to this dude.
If the redesign is creative enough I will give it a pass.
Personally I find it to depend on the game itself, so it's kind of case-by-case. When it comes to older games like on the NES, or games trying to emulate older systems, I give them a pass because it works to save on memory by just applying different palettes to existing sprites. For newer games with less limitations, or games that aren't actively trying to emulate the older styles, I really can only excuse a palette swap if there's some sort of addition to it (like, say, you fight a fox enemy in a forest, and later you find a white fox with more tails but the base is the same). If it's just a standard swap with no other changes, there should be some justification in its abilities or something like it being a rare creature (hello, shiny Pokemon).
Take for example the RTP slimes in the VX/VXA/MV packs, which are blue. I would assume them to be non-elemental or water-element. If I ran into a green or purple one, I would assume it to be made of poisonous liquid, and if I ran into a red one, I would assume it to be made of lava. If I saw a gold or silver one, I'd assume it to be much stronger, either offensive or defensively, and give tons of money or experience. If those changes are actually there, I'd find it rather cool. But if none of them have such changes, or are just the same slime with different stats? Then I would find that to just be lazy as hell.
My only personal exception would be region variants, where the same creature looks different based on where you would find it (a brown rabbit in a forest compared to a white one in a tundra, for example). If the stats are similar there, I can give it a pass because it feels pretty natural.
Found this old picture in the plastic case with my medical documents. I don't remember who this character is (I draw a lot of original characters and forgot about them very soon), but I like the design, may be I'll add guy in my game.