In my case, I prefer HGSS to GSC. And that's aesthetics-wise as well. In terms of a world that presents a very clear theme, I like HGSS's "Japanese" feel and look, and I think it made it more clear than GSC did. Music-wise, I can't make a decision, though.
In terms of favorite locations, I'd have to give it to RSE though. THe vibrancy of everything, the sheer variety of locations, the awesome soundtrack (dem trumpets), plus diving? Just great. Even BW, which has a nice "industrial" feel to it, owing to the New York setting, isn't enough to match that. Although, I would've liked to see snowy environments in RSE too (one thing which makes upper Sinnoh one of my favorite places).
Mechanics-wise, it's always new > old (can't wait to try out certain new things in BW2...). Story-wise... BW is still tops, for putting in effort to integrating your actions with the story (having gym leaders and Alder being mobile and interacting with you regularly, for example. Although DPPt had a bit of it with Cynthia). Dex-wise, I don't really judge entire gens like that. I have favorites all over (that's why I always look forward to new pokes). Music-wise...
(RSE = BW2) > (BW = RBY = HGSS = GSC) > DPPt > FRLG
Subject to change, of course.
And saying all this, I don't really dislike any game, since I enjoyed each and every one of them. That's why I stick around for so long, lol.