What? I thought Brinstar in Melee actually was one of the better stages for the series it was based on. The flowing acid (Metroid II), the breakable blocks/pillars (pretty much every Metroid game),.. It was (and still is) a fun stage. You are right on Rainbow Cruise, though: I don't recall any mountains anywhere in SM64 that had a little town in any of the courses (Mario Sunshine, though, was full of them..)
Now, for stages I'd like to see..
- A Wario Land stage based off the train stages from said game (I haven't played any of the other WL games, just the first one), complete with updated music (please, please don't let the remixes be as bad as most of the Kirby songs in Brawl..)
- Something based from Paper Mario.. An idea I had a while back was on Mount Rugged: the bridge in front of Klepto's nest. Klepto would occasionally appear and throw feathers (per his appearance in the game), and enemies from this area of the game could also make an appearance also.
- More Mario Kart based stages (I realize SSB4 is doing this somewhat). An idea I had was on raised platforms on DK's Jungle Parkway, the bridge in front of the big waterfall toward the end of the track (what's up with all these bridge ideas). I could see it working similarly to Fountain of Dreams in Melee, with the two smaller platforms occasionally disappearing, leaving fighters to.. fight on the bridge (but that would be more dangerous because of the race also going on at the same time, similarly to Mario Circuit in Brawl)
- A Zelda stage set in Dodongo's Cavern, on the bridge above the giant Dodongo's head (surprise). Keese would be flying around (and sometimes be on fire, and set the fighters on fire), and maybe the one platform would rise up to this level, occasionally giving another place to stand/land on.
I should go dig out an old notebook I know is filled with stage ideas