My favorite place in R/S/E in Hoenn would be Mt. Pyre. It had epic music, mysterious places, and the Red Orb and Blue Orb. The ones that controlled Kyogre and Groudon. It's also surrounded by water.
My second favorite place is the Abandoned Ship. I always wondered what that was about. The music was cool. Depressing, but cool. That's where I evolved my Marshtomp into Swampert, and taught my Swampert, Ice Beam.
My third favorite place was the Shoal Cave. I had a hard time getting the ingredients for the Shoal Bell (or Shell Bell, idk) lol. I always liked going there for the Snorunts too.