Personally, I find Gen III to be the weakest Pokemon Gen (Still enjoy it, though). I have two large problems with R/S/E:
1. There's next to nothing to do after beating the Elite Four. Gen II let you go through a second region, and that was on an 8-bit game. R/S were 16-bit, and yet here's all the post-game in them:
-S.S. Tidal
-Battle Tower
-Latios/Latias
-Raquaza
Emerald did rectify this a fair bit, but the post-game still felt lacking in my opinion
2. Too much water. Literally half of the routes in Hoenn are water routes, which I find to be a bit rediculous. I like the parts on land, but the water routes get so repetitive so quickly, especially when a lot of those trainers on the water routes have the same Pokemon.
FireRed and LeafGreen were good in my opinion, but I don't think they had enough changes from the original games.
I really like Gen IV, however. D/P/Pt are my third favorite group of games (G/S/C, then R/B/Y, then D/P/Pt, then R/S/E), and I find them to be a large step above R/S/E. Sinnoh felt very large and diverse to me. There were few water routes, there were a lot of designs I enjoyed, there was a lot of Post-Elite Four content, and there was Cyrus, who I quite liked (although Team Galactic as a whole was a bit odd).
And don't get me started about how amazing I think HG/SS have turned out. :P