I tried to think of more, but my memory's a bit hazy on some of the antagonists that came to mind, so I decided not to list those.



Zenos - FFXIV
People are pretty divided on Zenos, but I really like him. He doesn't really care about ruling the world and all that, he's not some scheming mastermind that sits back. He participates in conquest and goes to the front lines because he just loves the thrill of battle. He respects combat prowess and detests cowardice, and he's just overall a badass (albeit an evil badass).
stormblood spoilerPlus I like how in the end he considers you both his (first) friend and enemy. Like a twisted sort of kinship in finally coming across someone who is his equal on the battlefield.




Ouroboros - Trails series
Okay so this isn't an individual, but I decided to go with the orgnization as a whole rather than the many individuals in it that I love, both because spoilers and because I didn't feel like just filling this post to the brim with Trails antagonists.
Ouroboros has it both ways. It's a mysterious secret society in the background, pulling the strings that move the entire series for reasons that are still not entirely known, but also a collection of incredibly likable individuals that you get up close and personal with. Some are magnificently evil, some have their own tragic circumstances, some actually seem pretty kind and benevolent. The only thing they all have in common is that they're a powerful bunch who all have their valid reasons for joining.