The background music - Unlike the english one, you get to hear music AND songs from kanto to DP and movie #1 to #9. The way they used the music is really great too! It makes an episode so much better to watch than just 'uh.......ok<stares blankly at the scene........done'. I swear music is one of the reasons why i like pokemon so much. Take for example, in the episode 'Veilstone Gym! Lucario Vs Buizel!', they used Aaron's theme from the 8th movie, opening theme from the 9th movie, and the ending theme of the FIRST season. I tell ya, if its the english version, its gonna be those repetitive battle music again.
The voice actors(VA) - The english one really doesn't cut it. They all just sound so unnatural to me, especially Ash, although I must say Sarah has improved alot... The original voice actors are just wayyy better. Go check it out, a touching episode like 'Goodbye Pikachu', the part where Pikachu runs towards Ash. Ash opens his arms and attempts to embrace Pikachu while saying: "Pikachu!". I watched the raw version and it was touching, and then....i watched the english version and i was lol'ing(no offense). Its either English voice actor sounds unnatural, is inexperienced, or perhaps i just like the japanese one more ;) Basically i feel that the original voice actors put in alot of effort and emotions when they voice act.
OP and ending themes - You have RAP in the english version and i was like wow wtf pokemon RAP? I can't imagine having majority of the audience whos 6-12 being introduced to rap as a form of music, especially since literally every growing kid will watch pokemon. But i guess different cultures take it differently..bleh. The only english theme i like is Pokemon Johto, really well done imo. The rest is.....well kinda bad imo. The scenes in the OP/ending themes of the jpn are really great, some are memorable, some are touching, some are dramatic. Take for example
https://youtube.com/watch?v=m6W0p7ukazo&feature=related , nice memorable and a lil touching ending isn't it?
Oh and the way pokemon growls in the english version annoys me.