This is quite a funny topic to answer, because my opinion on the third generation has been extremely flexible over the years, and after playing through the games again and really taking a look at what it provided compared to the other games, its position on my favourites list has drastically changed.
My first impression of the games was honestly very good. If I remember correctly, the games were released very early on in the GBA's life cycle, so at the time, I had only really been used to GBC games when it came to quality. I'm not certain if this was before my brother got a PS2, which was arguably more impressive, since the portable consoles aren't really made to be as impressive. But yeah, I think it was before I'd experienced anything better than GBC, that I got to see the third generation Pokemon games for the third time. And while the graphics may not have been that impressive again, for someone who had only really experienced the older generations of Pokemon games, Super Mario Land and Wario Land 3 before, I was pretty amazed by what the games had to offer. I absolutely loved the new Pokemon, I loved the progression of the game, and I had a lot of fun with it. It was still in a period of time, where I wasn't fully aware of all the functions of the games, or even knew all the typing match-ups, so the features it provided didn't really wow me that much, but just the design-value and the gameplay was enough to leave me impressed. Unfortunately, I lost my copy of Ruby only a few months after getting the game, so I didn't actually get to play it all that much. My mom didn't want to buy a new version for me, so a lot of years went by before I truly got to play through the game again. I did watch others play, and helped them out at certain points, but I never really got to play it through myself. In the span of time that I didn't own the game, I got to play through Leaf Green, which was the last Pokemon game my mom ever bought for me, Diamond together with a friend, and a bit of Black after finding the wonderful world of illegally download ROMs (oops). I don't know exactly what it was that caused this, but at that point in time, I ranked the Hoenn as my second least favourite region, only getting passed by Unova. I imagine it might have been because my experiences with the other games had been much longer/better, so I just came to dislike the game for whatever reason. And for the longest time I went thinking that I didn't actually like the games. That was until the summer of 2012, where I found out, that one of my friends had a copy of Sapphire. At that point in time, I'd still not fully played through the region again since losing my game all those years ago, and since it had been a while since I'd had an experience with a Pokemon game on the actual console, I decided to borrow it from him. And I enjoyed it so much. It was the most fun experience I had had with a Pokemon game in a long time, and I found myself appreciating the more technical aspects of it more than I did as a kid. So Hoenn quickly shot up to becoming my second favourite region of all time, only being surpassed by Johto due to nostalgia.
Onto what I actually like about the games vs what I don't like. The main thing that I really like about the third generation games, is the way they completely reformed the Pokemon formula from what we'd seen in the two generations prior to it. I mean, the whole 8 gyms, e4, catch 'em all formula was still the same, but the third generation introduced an actual story to go along with it. In the first two generations, there wasn't really any actual story involved. You were just going through the regions, collecting all the badges, occasionally having to fight your rival, and stopping Team Rocket because the trouble they were causing was getting in the way of you gathering all the badges. The third generation completely changed that around, and tied an actual plot into the game. And while the plot may be kinda weak compared to later generations, it was still the one to start the trend. But yeah, it introduced "evil" teams that actually had motives other than stealing Pokemon, and tied the titular legendaries into the actual progress of the story without just being like "oh btw here's a wing you can go find this pokemon now". It used to legendaries to spice up the story, and really hype up the battle with the Pokemon. And while I did say the plot might've been a bit weak, it's still my favourite of any from the Pokemon games today, simply because it kept it simple while still being interesting, and you could honestly sympathize with the evil teams, since they just really believed that their motives were to better the world (despite giving them such intimidating designs).
Other things I really love about the games, is the way they hype the battle with the champion. In the first generation, the champion battle wasn't nearly as exciting because you'd already fought your rival multiple times before reaching him as the champion. In the second generation, you didn't get to battle the champion throughout the game, but he was the final member of the E4 from R/B/G/Y, and you barely even heard much of him, apart from when you infiltrated the Rocket Hideout with him. But in the third generation games, you met him multiple times during your travels, without outright being told that he was the champion, and he was involved with trying to stop Team Magma/Aqua, so you got the feeling that he was somewhat strong and important. And in the end, you find out that the person who's been helping you throughout the journey is the champion! It's not that it was really that hard to guess, but they don't make it super obvious like in generation 4 (where I think they outright say that she's the champion), but they still show him enough times for it to feel exciting.
I also really like the Pokemon in this generation. While a lot of them have been subject to critique, as well as people claiming this was where the era of good Pokemon designs ended, I feel like the third generation introduced some of the coolest Pokemon, along with a lot of creative ones. I liked pretty much all the starters, I really like the whole Feebas/Milotic evolution, even if it does feel a bit reminiscent of Magikarp/Gyarados, and other than that, the generation just introduced a lot of Pokemon that I just like for whatever reason. My favourite thing however, are the legendary Pokemon. I feel like this generation really did it right. While I really wish that Deoxys and Jirachi had been available without the need of events, I really liked how you got to find a lot of the legendaries. The way they involved the titular legendaries in the story was really cool, and made it way more exciting to battle them than just being told you can find them somewhere. Rayquaza was the first legendary where I felt like it was actually given a decent challenge to get to. Articuno had just been pushing around a few boulders to make you able to reach it, and Ho-oh was really just tedious to get to. But Rayquaza actually required a little bit of skill to get to, by being able to maneuver your bike over the cracked floor while not losing speed. While it may not be all that hard now, I remember I was one of the few who was able to do it when I was young haha. And when you finally reached Rayquaza, it honestly just felt really cool. The way the view of the sky was open, and it was just sitting there. idk I just always really liked that. And then there's the regis. I think they might have had the most elaborate puzzle in a Pokemon game to date, and I really enjoyed figuring out how to find them and catch them :D That's about it for the main things I enjoy
As for the things I dislike though, there also are a few of those. First is something that's already been addressed loads of times before. The amount of water in the region is ridiculous. It wouldn't really have been as big of a problem, if it wasn't because most of the routes were filled to the brim with constant Pelipper with supersonic encounters that were apparently impossible to run from. It's one of the main reasons I disliked the later parts of the games, because the last few routes and cities were all surrounded by water, and with the cost of repels you either had to empty your pockets, thus making you unprepared for the E4, or deal with constant encounters while just trying to progress. At least you didn't encounter Pokemon underwater unless you were deliberately trying to. I mean, going through the grass, it took ages to find Pokemon.
My only other big complaint specifically to the Hoenn games, is the lack of post-game content. There were the legendaries and the Battle Tower/Battle Frontier, as well as the secret bases, but that was about it. And considering the massive post-game that G/S/C provided, it was something pretty big the games had to follow up to, and they really didn't deliver. I personally never found the Battle Tower or Battle Frontier that enjoyable, and there was only so much you could do with the secret bases.
But other than that, I don't really have that many complaints. Obviously there's the things like the lack of the physical/special split, but that's an issue that applies to all pre-4th gen games, so I'd hardly say that's an issue with those games. Maybe also the insane amount of potential double battles that just become consecutive single battles, but I think that might have been fixed in Emerald iirc. I also realise I didn't mention contests, but that's simply because it was never really that stand-out to me. I didn't dislike them, but I was never too interested in them either. I know a lot of people enjoy them, and I think it's a cool feature, but it's just not something for me.