As far as boss fights are concerned vis-a-vis the ability to modify terrain, I think options exist to overcome that and to force fighting them in a specific arena. In fact, a hint of this exists already in Terraria: Corruption. While modifying corruption is possible, it requires an arbitrary tech level, and furthermore I don't expect it's a difficult premise to prevent the ability of placing terrain within a region as defined by a live boss. In Starbound, this posits at least two or three different contexts: you can either summon an alien boss and fight him in his ship (spawns something on the surface, like meteors); you can find an ancient horror deep beneath random worlds; or a mix of the two, where you summon some magic thing randomly on the planet - could be on the surface or could be in a floating sphere.
This would be in addition to bosses in the current Terraria flavor, where you're allowed to create an arena and have some control over where you fight a boss. This would allow for a few different flavors of bosses, although I agree that the 2d platforming genre is somewhat limited in possible options. I did like Neon's idea of riding a worm-type of boss as you fight it, instead of having constantly dig through the ground and pop out.