There are many problems with R/S/E. As many people have already stated, there were amazing changes and new features, but they failed with:
1- PokéContests: I hardly find someone who really enjoy them. Basically, the more useful a move was in battle, the less useful it was on a pokécontest (and vice-versa).
2- [HM 6]Rock Smash: Seriously, what were they thinking when they transformed Rock Smash in a HM? You were obligated to teach that to a pokémon and, well, it was a very weak move. (AND THEY KEPT FLASH TOO). The move deleter was there, but only at the end of the game.
3- Secret Bases: Yes, everybody expected they'd be something way better than it was.
4- Weather conditions: I loved the introduction of this mechanics, but it was ridiculous how it was made. At some places it rained forever and in others it never rained... Fixed climate conditions made this feature a bit fail
5- Unbalanced Pokémon: Maybe it's just my impression, but I think this version is the worst in balance. There were the weak ones and the tough ones, and only a few pokémon stand on the middle. Without mentioning the very-hard-to-get weak pokémons such as Feebas and Chimecho.
6- Money: I thought money was way too easy to obtain. I caught myself holding max money again and again. Linoone would caught a Nugget for me every now and then, and with the advent of Amulet Coin it was not difficult to get money. I could buy all the Protein, Iron, Carbos, HP UPs,... that I wanted.
7- Berries and PokéBlocks: As I already stated, I dislike the pokécontests very much, so the pokéblock system was completely unnecessary. Also, it was tough making a good pokéblock by yourself. The pokéblender NPCs were stupid and always missed lots of times. Also, the irregularity of grown of each berry made me sick. Seemed like they wanted us to play 24/7.
Although there were many innovations and real nice ideas in this version, the flaws were more evident than ever. I think thats the reason why so many people (including me) dislike this version.
WIN features:
Double battles, introduction of Abilities and Natures, way better Storage System, new kind of villains (Magma/Acqua), new kinds of pokéballs (fast ball, timer ball, premier ball,...)