In my opinion Gen 3 was by a long shot the best generation in basically all aspects. I like the Pokémon a lot, the region is cool, even the anime was better than the others gens.
When people say "hurr durr rbgy wer best" it's pretty obvious it's just the nostalgia talking, because to be honest RBGY are by far the worst. When they came out they were awesome, and they're still good games, but in comparison the other games just have so much more. GSC basically just adds another region on top as well as a ton of new Pokemon, as well as a lot of small things you can do other than battling - gathering apricorns, for example.
Not everyone liked the Pokémon design in RSE, but I think it's done well. The Pokémon don't look too complex, but they're more than boulders with arms. There's a lot of variety, and a healthy amount of legendaries that don't seem like they're only there to fill up space. Even then the games manage to give the player lots of exploration to do, in the form of the hidden Regi caves, Sky Pillar (in the case of Ruby and Sapphire), Mirage Island and tons of other things.
The remakes of RBGY, FireRed and LeafGreen, were nice. It was cool to replay the old world in modern graphics, and the addition of the Sevii Islands and several elements from more recent games gave it a nice mixture of recognition and surprise. I didn't enjoy the remakes as much as RSE, but they were still decent games.
DPP is where it sort of went downhill, in my opinion. The large amount of legendaries didn't feel natural. There were a decent amount of legendaries in RSE too, but they all felt like they had a purpose, or otherwise were very difficult to find without a guide, such as the Regi trio. However in DPP Pokémon like Heatran and Manaphy made a debut, and they just didn't feel "legendary" to me. The region itself felt more modern than in previous games, with a lot of ... metal everywhere, which didn't really feel welcome after playing through the previous games.
The GSC remakes were another story, though. The games kept the traditional look of the original GSC while adding a lot more to do and of course, compatibility with newer games. I didn't play these as much as DPP, but I still enjoyed them more.
Theeeeen there's White and Black. While they just continued to modernize the look of the game as well as playing with the camera angle in ways that make me nauseous, I still liked them. The lack of Pokémon from previous generations was a little annoying since Gen 5 doesn't have a lot of familiar type combinations - it seems like Nintendo were going for new, weird combinations that haven't been introduced before. This would be cool, but I'd still have loved some familiar faces to fill my party with.
BW2 fixed this problem by introducing older Pokémon to the wild, which I think makes it superior to its prequel. I like the fact that you actually live in a city as opposed to a town with three houses, as well as the idea that Unova is completely fucked up. It blows new life into the region and makes it cool to explore it again. I did think the story felt a lot longer in BW2 which I'm not really a fan of - I feel Team Plasma's ambitions were already explored to their full extent in BW. A lot of the things you have to do in the story was very tedious, too, such as the stuff aboard the huge zeppelin thing Team Plasma uses.
In conclusion I think the Pokémon games rank like this, in order from worst to best: RBGY - DPP - FRLG - GSC - BW - HGSS - BW2 - RSE