I've almost allways believed that all of themes fit in someway shape or form...So its hard and maybe impossible for me to really think of one that didn't fit. lol
About sinnoh... Ever notice that besides route 209 and rowan's lab theme...most route theme's were Jazz like (even the game corner)? I originally didn't care for most of sinnoh's route themes... then i acutually sat down for more then two seconds after the gen switch and found out I really missed the peaceful yet happy feeling most of them tended to give me. D:
I like ALL of the gym battle themes (they are all fun to listen to, and they're NOT not catchy)...but I beleive sinnoh's was the worst, followed by Unova. (Unova only wins cause of that DAMN final pokemon music. Thats still awesome.), then kanto's, then hoenn's, then johto's is my first favorite. but that's all remixed up when it comes to the remixs. HGSS's johto gym battle theme was my fav, and still kinda is, but the orginal in 8 bit never appealed to me...lol I'd put the 8 bit original version of the johto gym theme WAAAAAAAAY in the back. lol
Alder's is the only champion theme that was sort of meh to me. lol I just... didn't like it. I mean, its not bad to listen to...but Gary's felt like he thought he was the best of the best, Lance's/Red was also pretty epic in it's own right, Hoenn had that AMAZING drum line which I can never enjoy unless I'm wearing headphones, All of cynthia's versions are really cool. the first two being mystic...and the world tournament one having that guitar replacing some strings or something...GOD I love that guitar...<3...
Even Iris's has a good feel to it...and I liked the change to be honest...Alder's theme just kinda died on me. Which is funny considering he's one of my favorite characters D:...(I will totally end up being like him when i'm older. XD)