Pokemon has a lot going for it in terms of geography. I could rave on and on about what I like or don't like about just about every town, cave, or route. (I wont though, lol)
What are your favorite areas?
Me? I love Johto as a whole, it's got this whole "old country" kind of vibe to it with the architecture, but my favorite part about it is probably Olivine City. I just really like the whole "coast city" thing it has, and the lighthouse.
Lavender is really great, love the creepiness of the whole town. Even Mr. Fuji is kind of off putting.
Hoenn, oh Hoenn. I love so much of hoenn but my favorite is probably Fortree. I love it, just, a city in the trees, and the tall grass routes right below?
Don't remember too much from Gens 4 or 5. For 4 I'd have to give it to that one beach route, between the rest house and...whatever was West of it. >_> For Gen 5 my favorite area was probably the undersea ruins. Felt so cool diving in there.
I love Johto. That's the region I would want to live in. Specifically Ecruteak.
It's a nice small town with some cool local customs and culture, but it's still a short walk to the beach at Olivine, the big city of Goldenrod (which is also a great way to get to Kanto) and hell, if you have a surfing Pokemon, you can take a day, pack up a picnic and go to the Lake of Rage.
Don't forget to check out my MegaTen themed webcomics at http://www.drunkduck.com/user/Strain42/ (Currently Updating: Persona 4TW Add-On M-F)