I played Gens 1 and 2, then started again with 5, went back and played what I missed and then played 6.
What has gotten better:
-Battle mechanics
-Graphics (duh)
-Depth of pokemon. I find the idea of IVs/EVs etc to be very appealing, granted I hate how you obtain good IV pokemon atm.
-Quality of life things like the Pokedex actually having uses (finding Zapdos post game was kinda neat).
-Mini games (not all but some). I think the EV super-training is a solid addition, so is the berry farm.
-New pokemon seem to be given much more attention than older new batches (lol ice cream cone pokemon)
What has gotten worse:
-Story. Yeah it has to be a kid's game too, but that doesn't mean to story needs to be borderline mouth-breather style. I recently watched Pokemon Origins, and while I felt it was rushed and albeit predictable, I felt how the characters interacted, and their motivations were much more authentic than what we have today visa vie the games; and the catch is that mini-series didn't have anything that would be unacceptable/not entertaining to children. Make the villains actually seem villainous, you can accomplish this without having them do gruesome/terrible things in-game... essentially they need to seem competent and have a non-moron objective (see team flare).
-Difficulty. This one is sooooo easy to solve, simply put different settings in at the start of the game. Easy (what X and Y are now). Normal (No exp share, slower leveling, smarter AI for trainers). Hard all of what I just mentioned + very punishing pokemon load outs for Gym Leaders/Trainers, make catching all the pokemon that you encounter on your journey serve a gameplay purpose and not just a "well if I wanna fill up my dex post-game I might as well get all the wild route pokemon outa the way".
-Level design. Its just too linear, I enjoyed the aesthetic of the Gyms + a few of the caves, but I had no actual choice in how I wanted to progress through the game. Given how easy the Gym Leaders are in its current incarnation there is no reason why it can't be a bit more open world. I don't think this would add to "confusing" the younger player base either, everyone knows you need 8 badges, simply labeling which cities on the map have gyms + maybe their level range would be sufficient.
-HMs. Why are these still ingame? Why can't my water pokemon swim without me giving it some PITA hard to remove TM? Why can't my Machamp move a bolder?
-Over focus on the legendary pokemon. I prefered the legendary pokemon being rare encoutner or dungeons; it feels forced that it's always intertwined with the incompetent Team lol.
X and Y are def going in the right direction. Their online features are very well thought out (minus the fact that it got burdened with Nintendo's FCs, but that isn't really gamefreak's fault). Most of the changes they could make easily (minus the story as I suppose they are contractually obliged to keep it kinda close to the anime).