Oh God, there were rather many little things which made the game not so good experience for me and why I like D/P/Pt better. Let's list something...
-The lack of VS Seeker. The phone call system. ARGH! *frustrations* Seriously, WHY there was NO VS Seeker in the game?! It makes training so much easier!
- Voltorb Flip and the fact you cannot purchase coins. Goodbye Game Corner TMs
- If you either run, surf or drive a bicycle in a place where you can encounter wild Pokémon, you'll encounter one in every patch of grass. If you don't happen to have Repels, going somewhere quickly is pain
- You get Togepi in the beginning, but no Togekiss until... well, pretty late in the game
- You can grow only 4 Berry Trees at time. I would have liked to grow them much more!
- Evolution Stones are pretty hard to get but not as hard as in B/W and you can transform them from D/P/Pt where they're easier to get
Well, those are the most annoying things that come into my mind. I also have this feeling that there were much less different wild Pokémon than in D/P/Pt.