Fire Emblem didn't get an "iconic" location, it just got a standard castle.
I think Advance Wars would get the same sort of thing... just a standard grass-type battlefield, with tanks and stuff rolling around in the background. Possibly with an artillery hazard, dropping exploding shells onto the stage.
I agree with the lighthouses idea for Golden Sun, although, it doesn't look like Golden Sun's going to get repped at all....
Pikmin should get the Impact Site from the first game with Captain Olimar's ship in the background. When the match begins, the ship should be broken-down looking. As the level goes on, teams of Pikmin come and add parts to the ship (about 1 every 30 seconds). If you manage to make the match last for 15 minutes, all 30 parts are put in place, and the ship takes off!
As for Sonic, it's got to be Green Hill Zone. Although, that level hasn't ever been seen on a Nintendo console, so it might be Angel Island or (god forbid) Station Square...