I've completed the game twice over, and the hardest bits are always:
Charizard (rly annoying, i'm stuck on that now, and i just got the manaphy egg code for the first time ever)
Salamence (23 loops, AND resistance to Minun??)
Pupitar/Larvitar/Tyranitar in the Go-Rock Squad Base
Where do you find the Regis???(saw in first post)