I like to look at gen III and think I just didn't enjoy it as much as the others, rather than it being staight up "bad". I would never say it sucked, but it did drop the ball on some things.
Too many water routes, no day/night cycle, and the complete lack of postgame content (fixed in Emerald) are my big complaints of III, and the only ones I really feel are legitimate. And even then, the third gen was a reboot for the series and laid the foundation down for the next ten+ years of the series. It was a change, and people don't like change. There were a lot of things that rubbed people the wrong way about gen III.
Even so, the hate gen III gets is really unwarented. It really is the same game as the ones that came before and after it. If you liked one of those, then you probably liked gen III somewhere down the line.