Pretty sure I don't see much complaining outside of the podcasts about this franchise. They actually made A LOT of changes this generation, if you look at the details of the game. Could they have changed a few more things? Sure, but believe me, they changed more than enough.
I liked the menu system of Soul silver/Heart Gold better though, and we lost wifi Battle Tower. Those have been my only two minus that are at face value. I'd get into how there are hardly any hot spots for Special attack and special defense EV training, but that goes over people's heads...