I'm 22 now so RBY was my childhood. Obviously I have huge nostalgia for the games and it is difficult for me to give a fair opinion but I can also appreciate that they are technically poor, even for the era they came from. The battle mechanics were unbalanced and often bugged, the AI was bad to the extent that you could breeze through the elite four while underlevelled by ten to fifteen levels and without using items, and of course, the glitches (in fact I reckon Missingno probably contributed heavily to these games' legendary status). But it is pleasingly non-linear in a way that the newer games can't really match - this meant you could be really over- or underlevelled because you did stuff in the wrong order, but it massively enhance the replayability. I guess it's sort of unique in video game history in that it was sort of this surprise monster hit, and hence probably not as much care and effort was put into it because the makers didn't expect it to be as popular as it was.
GSC cleaned up their act quite a bit. There was actually a story of sorts, more than in RBY at least where stuff just happened, but it got the balance of story versus freedom right for me. The battle mechanics had been made deeper and the AI bosses better, you could still do most of it in your sleep but it was an improvement. But they actually put a lot of effort into fixing the flaws the first game had. The postgame was extensive - in fact, it was almost another game, which you could do in pretty much any order you wanted. And everyone remembers Whitney's Miltank, which shows that even though they did a better job than the first generation GameFreak still hadn't quite mastered the art of giving the games a good progression of difficulty.
I never had a GBA so I haven't played RSE much but these seem pretty divisive games. On the one hand it improved so much from the previous game: battle mechanics, graphics, bad guys who actually had a motivation rather than being token bad guys (granted their motivation was stupid, but at least it was there). A lot of people don't like the designs, but honestly, Hoenn was a tropical region, and in the real world a lot of tropical animals look batshit crazy, so I think they are justified. However, for me the game imposes linearity (like that bunch of Wailmers that are randomly blocking your path with no explanation) and then tries to create an illusion of freedom by making the routes so huge (especially the water routes that go on forever) that you just get lost. RSE had a lot of good things to it but for me was less than the sum of its parts.
Again, in DPP battle mechanics were sharpened. Can't remember too much because I haven't played it in forever. It had cool stuff like the distortion world, but also annoying stuff like the foggy areas that wanted to make you rip your hair out. Team Galactic were more credible antagonists than anything that had come before, and they had some pretty kickass music too. I felt the sense of exploration had been toned down in this one though - it is pretty linear.
BW is another generation for which I have mixed feelings. Unlike RSE and DPP there weren't really any groundbreaking new battle mechanics. Stuff like reusable TMs and the modified experience formula were nice though. In fact, this new formula puts a cap on how underlevelled you can become because you will level faster if you are underlevelled, and level slower if you are overlevelled. This means we can let the game be a little more open-ended, right? If only. The linearity of this game is thrust in you face - that one bit where there are people who are "dancing for no reason, one day we'll stop dancing for no reason" maddens me. They are trying to turn the crappiness of their game into a joke (I think), but all it does is focus the attention on how poorly Unova is designed. True, they are trying to tell a story, and you can't easily tell a story out of order, but the story isn't really good enough to justify in my eyes, and I found myself scrolling through the text in the cutscenes without reading it. The decision to use only new Pokemon sounded cool, until you realised how many were pretty much copies of previous-generation Pokemon in both design and battle properties. That said, when it got it right, it got it right. The postgame is actually interesting with some neat sidequests. The overworld music is the best in the series, in that it actually matches the atmosphere of the area, rather than being generic music as in previous games. The victory road gate, with the music that builds one instrument at a time, is so awesome that it almost makes up for the rest of the game's flaws single-handedly. The other thing that was great about this game compared to previous generations is that the ordinary trainers are more challenging, whereas in previous games only the bosses would ever even make you think, which makes the games feel less grindy.
Not played XY yet, that pleasure still awaits me.
Overall, it's really tough. I think I'd give it to gen II, which seems to deliver the most consistently across all aspects.