Hoping its not too late to reply to this topic since the last post on it is a bit old...
...But my favorite dungeons are Shade's Gym and Byxbysion so far, with Byxbysion being the last one I've made it up too thus far in the game. As far as a least favorite at this point, it would be the 3rd Tangrowth Machine, the one where the Salamance girl gets called a brat, even tho I liked the zone itself, I felt like I had JUST did this not 5 mins ago, and now I'm doing it all over again.
For what I like in areas, I love sub stories and side quests, good BGM (both of which this game has in spades), but in some places I wish encounter rates were actually a bit HIGHER (cept for that one zone where you save Cain, that one was a pain, but the other zones left me spamming sweet scent).
Oh, one thing to make any zone perfect, Absol. Absol can make anything awesome. Completely unbiased opinion.
*Edited to update that I ended ep. 9, and if there's more stuff like the steelix sub-story, that would be friggen awesome.