I feel like gen 3 was overrated, if anything. I like it because it brought new battle mechanics to the scene (abilities, natures, etc.) but I will always have a deep-set dislike for the gen because it very nearly made me drop the Pokemon series for good. :x It always baffles me when so many people go on about how much they want a remake of RSE because the games were so good when I didn't really enjoy them at all.
I disliked a lot of the Pokemon designs, initially. They were very different because, iirc, Gen I and Gen II was sort of made in tandem with each other so the designs flowed very well between them. But in Gen III, the designs started getting more complex. Now, this isn't a bad thing--I actually love a lot of Gen III Pokemon nowadays--but back when I played it, I just wasn't very impressed with a lot of Pokemon. I also didn't like any of the character designs so that didn't help either. XD;
I hated Hoenn. I still hate Hoenn. It's filled with caves and mountains which I dislike at the best of times but surfing is my least favourite thing ever and pretty much all of Hoenn is water routes. Or it sure feels like it, anyway. D: Diving was annoying too and I agree with the people who mention that the currents just made it annoying to collect everything and battle everyone. I don't like having to go through routes a lot and that was pretty common in this game. (Even jumping down ledges made you go back a lot in this game to get everything.) I didn't feel like the route designs were very good and I also didn't like any of the cities or dungeons, haha.
I also didn't like FRLG at all, which I associate with Gen 3 as much as I associate them with Gen 1. :/ I was excited for them because of the nostalgia, but when I actually played them, I found I didn't really enjoy them and I'm not even sure I finished them last time I tried to play. Overall, the GBA entries in the Pokemon series didn't work well for me. If I hadn't been a member of PC from before they were released and felt obliged to stay in the fandom to stay here, I would've dropped the games after playing Ruby and FireRed. I'm glad I didn't because Gen 4 went on to become my favourite but I just... never got into Gen 3.