Kanto
For the first generation, I'm honestly not sure at all. I wouldn't say that the gym leaders didn't stand out or appeal to me in any way, but I just never really got any opinions on them. I guess it's mainly because there wasn't ever really much to characterize their personalities through, so favourite/least favourite would almost always have to be based on their difficulty levels or their team, but I just... usually refrain from judging characters on that. There wasn't much either to really drag them apart from each other conceptually, apart from how they usually just had something related to their typing-specialization to them, which was almost always expressed through the gym anyways :p
In the end, I reckon I'd have to go with Blaine though. It's not because I specifically like him more than any of the others, and looking at him as a character, I think he's actually one of the least defined. But I really enjoyed his gym, with the Pokemon trivia questions and whatnot. Fire types used to be my all time favourite (partly because I loved them on my team, and usually had something to counter them as well ;)), so that just made it even better. And while I may not have liked the Pokemon mansion itself, I liked the concept of not just making the gym something you can walk into, but actually having your prove that you're capable of taking on the challenge. And then there's Blaine himself. As I said, he's not very much a defined character, but for some reason, I've always really liked old people in games, since they often have interesting characters, have some special powers, or just have amazing beards/mustaches, and even though it's only really the mustache that plays through with that when it comes to Blaine, just the fact that he's an old man gives him a plus :p
His team was also super interesting and fun to battle. Like I mentioned, I really used to love Fire types, and his was just full of all the awesome Fire types, which made the battle so much more enjoyable. And while he may not have been hard, as long as you had a relatively decent Water type with Surf, without it, he proved to be quite the challenge at times. I mean dat Arcanine and Rapidash. Glad I brought Burn Heal ;)
But yeah, that's about what makes it for him. I guess one last thing that's basically the icing on the cake, is his style in fashion. I mean that pimpin' hat in HG/SS though. What a classy old jeezer ;)
Johto
I could just go ahead and be biased here and say that Falkner is my favourite because birds. I mean, birds a pretty darn cool. But really, he kinda falls into the category of not very defined characters like most of the first generation gym leaders, and I just never really found any reason outside of the Flying types to really like him as a gym leader. I saw the episodes of the anime featuring him as well, and neither his little side-plot nor the battle between him and Ash really stood out to me. And I actually seem to vaguely recall him being a new gym leader in the anime as well, so yeah, even less experience on that front :p So while he'll still be at the top of my favourites of the second generation list entirely due to them birds, I can't really claim him to be my favourite.
Nah, I'm actually gonna have to go with Pryce here. AND I DON'T KNOW WHAT IT IS WITH OLD MEN, K! But yeah, again, from a viewpoint of the games, he never really stood out much either, and his team consisted of Ice types, so he was kinda doomed to never be a threat (Sorry for Ice type fans, but they have waaay too many weaknesses, and when controlled by the in-game AI, there's just not much threatening about them :(). But his anime appearance, unlike Falkner's, really stood out to me for some reason. I don't remember if anything ever really hinted at it in the games, but I always kinda pictured him as a nice guy, but when we got to the anime, he was completely cold-hearted (you know, because ice. clever writers!), and he didn't care much about his Pokemon. This came from an experience in his childhood, where he thought that his best poke-friend, a Mamoswine I believe, ran away from him. It turns out however, as Ash conveniently found out, that the Mamoswine had gotten lost or something, and had been frozen in a cave for what must have been like 50 years. But yeah, they melt the ice surrounding the Mamoswine, and Pryce starts caring for Pokemon again, and became the character I actually pictured him to be. And I think that's part of the reason I liked him so much. That I actually managed to get a picture of his character that they presented him with in the anime as well, and that aside, he also had a really touching side-plot to him, which I reckon we rarely see with a lot of the side-character gym leaders. But yeah, that's pretty much the reason I like him so much, but I guess that's mainly because the gym leaders of Johto never really left much of an impression on me :p
