I loved Gen 3. My only real complaint was the removal of the day/night system. I even liked all the water as, previously, Surf felt a bit more like some sort of special boot needed to travel over water instead of its own, unique, area. --- If you love a person, it doesn't matter if they cheat. If you love a person, you won't cheat.
I really liked these games. My biggest complaint for the games would be too much water.
However, my complaint for the 3rd gen over all is the way they split up pokemon. I like that ru/sa have some old pokemon, but the majority are new pokemon. Then when FR/LG came out, I figured the rest of the missing pokemon would be there. Which still wasn't the case. You still have to get colosseum or emerald to get access to many missing pokemon.
Other than that, I really liked the games themselves and everything they had to offer. I think they're the best generation of games.