Good question. It would depend on the game imo. Link from Zelda is a pretty good character design wise. Changing somewhat over the years from game to game.
As for a game/series, I'd have to go with the Goldensun series, it stood out to me in regards to both character design, world design and in the soundtrack as a whole. It was really vibrant to be honest.
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In my opinion, Lara Croft in Tomb Raider (PS4 version) is the best I've ever seen.
I disagree. The PC version of Lara looks the best. PS4 Lara doesn't even look like she's properly reacting to the situation she's facing, something that even the PS3 version accomplishes.