Red / Lance are my joint favourites, with Steven Stone in 3rd (but really, any of the Gen I-V Champions bar Iris could have come there, they all have their strengths and weaknesses).
Steven is mainly in 3rd because of nostalgia - Emerald was my first game, I didn't even know he had been a champion when I first met him in the game like anyone who had played Ruby / Sapphire would do. I just really like the character; He's got pretty unique interests outside of battling compared to most characters in the games, he uses some damn cool pokémon (Metagross and Aggron are standouts), and he's completely optional! I only found him by chance the first time I completed the game because someone told me you could go to space so I was looking all around Mossdeep (that white rock was a real mind**** from GameFreak) and when I found Beldum I decided to train it in Meteor Falls, eventually noticing the extra cavern. Took him on with nobody over lv. 60 aha
Red is tied with Lance for a couple of reasons - firstly, they both have the same outstanding battle themes in Gen IV. His design's a classic, as are his pokémon (although I think I would've liked battling an Espeon instead of a Lapras, having us both equally damaged by the Hail at all times would make it even more epic in my opinion), and his lack of dialogue is a great callback to his previous as possibly the most silent of player characters if that's possible to rank. Plus I mean exiling yourself on a mountain because nobody else is strong enough to bother to fight? Badass, and I think we've all had that desire in a game to be allowed to take on the role of Champion and actually be challenged by other trainers - this is the closest you can get.
Lance meanwhile - the guy's the original Dragon trainer, his teams are some of the coolest ever assembled, and he takes on such an active role against Team Rocket, especially in comparison to in RBGYRFrLg where Red is seemingly the only person who even cares about Kanto being more crime-ridden than Gotham during Batman's childhood. Having multiple Dragonite is such overkill as well, kinda makes him seem a bit overconfident in his belief that he can simply overpower everyone with cool, and who doesn't like their heroes flawed? His only drawback is the capes but hey, he originated in the 90s and if we forgive real people why not him.
Sorry, bit of a long one but I really like these guys.