For me, it was a case of broken expectations. I got Sapphire expecting to have new features alongside the old ones--three regions to explore instead of two, the original 251 Pokémon plus 100 or so new ones, the Day/Night system, Team Rocket's return, etc. Instead, so much of that got taken out that I hated the games. The generation has grown on me, mostly because of FRLG and Emerald. Now I think Hoenn has some great area designs and some awesome Pokémon, but I still have issue with a lot of their Pokémon and I still find the water routes incredibly tedious (water Pokémon aficionado though I be) and the whole Team Aqua/Magma storyline stupid. Also, like others have said, outside of Emerald there is NO postgame (which was especially disappointing since I was hoping to have another region to explore afterward). I still think R/S are the worst of the main series games (aside maybe from D/P, which I haven't played often enough to give a good judgment), just because they were lackluster. Emerald is a great game, though, and I do enjoy playing FRLG.
As for the Pokémon themselves, I think there were far too many clones. I mean, Hoothoot/Noctowl and Sentret/Furret were similar in function to Pidgey/Pidgeotto/Pidgeot and Rattata/Raticate, but they were different enough in design and moveset to make them stand alone. On the other hand, the Taillow line and the Zigzagoon line just seemed like blatant ripoffs of previous generations, as did the Wurmple line, the Skitty line, and the Corphish line, among others. Some of the Pokémon were pretty lackluster as well (i.e. Luvdisc, Chimecho, Wailmer, etc.), although this region does include many of my favorites.
And overall, I think there is beauty in simplicity, which is what made the first two Generations so awesome. As the generations have gotten newer, the Pokémon have come to look more and more like Digimon or Yu-Gi-Oh monsters, and Hoenn was kinda a midpoint between those two extremes--they were simpler than the newest generations but still lacked the simple elegance of the older ones.
Still, Blaziken, Sharpedo, Absol, Breloom, and Milotic (among others) = win.