It's difficult for me to decide which Generation's graphics I would call my favourite. Not only can the quality of graphic styles vary greatly between games of the same Generation (e.g. Pokemon Pearl vs HGSS), but my 3 favourites also seem to be different and incomparable due to console limitations (which gave them both strong points and flaws).
Even though I only started playing Pokemon when I was already 18 years old, so nostalgia can hardly count as a contributing factor as I've never played this Generation Pokemon game, I really love Pokemon Crystal's spriteworks. It took me a while to notice them at first, because I usually only paid attention to the Generation that I was playing. At some point an artist pointed them out to me, and since that time I've started noticing their brilliance whenever I look up sprites/models of a Pokemon and glance over this game's artwork as well. I especially like the dynamic poses, and how most Crystal sprites just feel very 'spot on' for me.
When I played SoulSilver, my very first game, for the first time, I didn't really notice how amazing this game's graphics were. But then when I completed it, and played Pokemon Pearl, I realized that I had just been spoiled. Pearl was a pain to play through for me, especially because of the graphics. I kept longing for SoulSilver, my 'home'. Eventually I had to make the transition to Black and White, but it didn't connect quite as well. I disliked the animated sprites (especially the backsprites, as has been mentioned by someone else in this thread), and everything felt sort of 'cold' to me (but that could also be Unova instead of the graphics). HGSS looked seamless to me, and played seamless. Some of my favourite sprites are from that game, and certain/most places in the overworld were also marvellously done.
Generation 6 brought models instead of sprites, and while I was
very sceptical about the graphics at first ('Why does everything have to be turned into 3D now??'), from the moment that I bought a 3DS and played XY for the first time, I fell in love with it (proof that love at first sight exists). While it is not quite as seamless as HGSS was, my enjoyment went up by 3 stages. Before, most of the games were about collecting for me. There was a plot, and there were characters, but I could never connect to them or the story. I now suspect that this was because it were just small overworld icons talking and sometimes pacing back and forth. I hardly felt any emotion from it. But now in the 6th Generation games, the characters have facial expressions and special mannerisms, and I can finally experience the story. I like most models, and the colours don't bother me at all, because I think it fits better with the way the rest of the game looks. There are some Pokemon that have had unfortunate transitions to a model instead of a sprite, but in the end it doesn't bother me or limit my enjoyment. There is one part of
Kalos Route 10 that feels odd to me though, and I'm annoyed that I don't get why this was handled this way. Did someone's hand slip? Or am I just not looking at it the right way? It's the part where the sandy path stops and the part with the stones begins. The transition just feels so weird to me.
I love ORAS as well, but there are some things that I'm not sure about for this game as well. One is how Mt. Chimney looks when you're soaring (or in the intro scene). Two is the bar that displays specific kinds of game text, the one with the lazy red/blue gradient and blocky/pixely kinds of things on the side. I'm not going to take a picture of what I mean, but I can
link to an image I found through Google that has part of the bar that I'm talking about.
In the end I voted for Generation VI, for being most consistent in quality between this Generation's games, for finally enabling me to care for the storyline and allowing me to get to know the characters better, for immersing me into the game thanks to more natural camera angles, and for looking lively and anime.