I don't have a clear favorite, but there are a number of spots I like.
Gen 1:
-Pallet Town: Not because there's actually anything to do there, but I like the music, and I like that it's where everything began.
-Vermillion City: It's on the water, and is an interesting hub. I also think of it as being the last part of the early-mid-game (I think of start to Pewter as early, Mt. Moon to Rock Tunnel as early-mid, Lavender through the rest of mainland Kanto as late-mid, and Cinnabar (post Silph Co.) to Indigo Plateau as late), and I feel like my team is really starting to get established by the time I reach there.
-Fuchsia City: Home to the first Safari Zone, and for whatever reason, I've spent a lot of time there.
Gen II:
-New Bark Town: Again, I like starting towns.
-Goldenrod: So much to do!
-Ecruteak: Not sure why. I guess I like the rustic feel.
-Mount Silver/the route outside Mount Silver: This is the culmination of my journey, and I recall doing a lot of training here when I was younger. It also represents the culmination of my efforts in both gen I and gen II (as Red is the champion from Kanto, and the GSC protagonist has finally reached the journey's end and become the best trainer out there).