Why only Totodile and Chikorita? I know that Cyndaquil is quite the fan-favourite of this generation, but I don't think it should be left out :p Unless it was to compare the two underdogs, in which case I don't really see Totodile as an underdog. Chikorita is the only one that has really gotten blatant hate out of the three, and it's not because it's really a bad Pokemon, but more because of how badly its typing matches up with the gyms of the region, being weak to 3 of the gym types. Between the two, I'm going with Totodile though, mainly because of the reason above. I really love Chikorita design-wise, but I've always been pretty reliant on my starter Pokemon, so I've just never really been up for the challenge of using Chikorita. I think I may have gone through the game with Chikorita once, but I think that's pretty much why I never chose it again. And the spot for my favourite has just always pretty much been between Totodile and Cyndaquil, as they're both awesome, both design-wise and when it comes to battling. I can easily say that the second generation has some of my favourite starters, but then again, that may just be bias. I've just always like them though :p
I'm gonna be totally honest here, despite my love for the second generation, I've never found the E4 to be specifically memorable, and could only remember the reappearing characters from the originals when playing through my brother's gold again a few years after my friend lost my Gold, so Will and Karen are totally out of the question when it comes to favourites :p
But yeah, my favourite E4 member is definitely Bruno, and that goes for both generation 1 and generation 2. I don't know what it is about him, but I've always found him to be pretty cool. I think part of it is for the fact that I actually thought he was the one you got Tyrogue from, and as such felt like he was more involved with the character, and I guess just because I liked his team so much. Overall, I don't really have much of a specific reason for why I like him, I've just always felt like he was pretty chill :p Oh, and I definitely started liking his character after reading through the first arc of the Pokemon Adventures manga, (
SPOILERS for anyone who hasn't read it and plans to sometime :p)
As for the one I found to be the hardest, I guess it would have to be Koga. The Johto E4 wasn't really that hard, and the only one I ever really had problems with was Lance, solely because of the fact that I had no idea what Dragon was weak to, and only knew that his Gyarados and Dragonites were weak to Electric type moves. Thankfully that was half his team. But yeah, Koga. I honestly don't remember why I had such a hard time beating him, but I'm pretty sure it was just that darn Muk. I just remember I've always hated Koga, and I honestly wasn't happy he was promoted to E4 member xD
As for which E4 member would have the best chance of beating the others, I reckon Will, just because he has an edge on Koga and Bruno with his Psychic types, but Karen might be able to wreck him. Either way, as I said, I never found the Johto E4 to be that memorable, so don't really have much input on that :p