This thread is great.
RBY: Misty, everyone has already mentioned why. Now whenever I do a R/B run I make sure to have gyara. Honorable mentions goes to Lance in Yellow, Dragonite hits like a locomotive.
Stadium: Lance, amnesia snorlax that explodes, great. Plus he loves to spam wrap/fire spin. Ugh. Agatha, gengar and zam on the same team. Jynx and Gyara too, the fight can be hellish.
G/S/C: Meh, whitey isn't that hard. More annoying than anything. I'd have to say Red and only because your levels probably don't come anywhere near his.
Stadium 2: Fuck little cup.
R/S/E: Liza and Tate, I just never seem to be prepare for that one. Claydol needs to die quickly too because it just spams EQ all day. Honorable mention to Brawly and the rival battle above slateport. Swampert trolls the rest of the game.
FR/LG: the Rocket who is trying to get the random gem thing from the scientist. I don't even remember why this fight is hard. just that it is.
Colloseum: Nascour and Evice. Not ready for that battle, even with tower grinding beforehand and their shadows are HARD to catch. Succeeding in catching them doesn't make the fights any easier either. Honorable mention to Miror B, fuck rain dance
XD: The moron with the Shadow Zangoose. You access him early, I did so by mistake, and got obliterated by that thing. Honorable mention to Gorigan for EQ spamming when I have no flying types.
D/P/Pt: Cythina, hands down. She just doesn't have any really exploitable weak points on her team and garchomp is by far the most dangerous thing you have encountered up to that point. I had a team of Garchomp/Gastrodon/Infernape/Bronzong/Roserade + HM slave (Level 55-57) and still had trouble. With SR in play. Honorable mention to Crasher Wake, unless you have a grass type, then he dies.
HG/SS: Doing a play through right now and nothing has really jumped out at me. (Dragonair/Meganuim/Togetic/Quasire Level 39-40 about to fight clair) Gonna have to say Lance rematch since spamming an ice type isn't an auto win anymore. Honorable mention to Red for the level 88 Light Ball Pikachu and hail+blizzard spam.
B/W: This is a joke right? I abandoned my team and starter in favor of some of the newer pokes half way through and still completely overran the E4 and Ghetsis. The lucky egg means I don't have to bother grinding anymore. Post game I can immediately catch a level 50 Dratini that has both DD and Outrage?! Yea, piece of cake.
Normal mode: I swept the ENTIRE elite 4 with Zoroark. Including the champ and marshal. Genosect before the 1st gym. Well, that will learn me for using event pokes in game.
Challenge mode: This is more like it, but still too easy. Especially compared to the earlier games. Part of the problem is that you can assemble a pretty good team very early. Luke, maggy, Arcanine, starter/haxourus, two slots for w/e. Honorable mention goes to the post game battles of Colress, Benga, N and Cynthia. Although Cynthia is somewhat of a letdown compared to what she was in gen 4.
Any problem can be solved with the proper application of explosives.