I've only skimmed this thread, but I kind of agree that it would be cool to develop more games that give you the freedom to avoid situations and possibly find other ways around them. (one game that I think did the multiple paths thing pretty well [if a bit obvious] is good ol' Deus Ex)
There are a few bosses you can run away from in Aquaria. I believe all the optional bosses can be run away from, and I think with the first "required" boss (the energy god that you have to kill with the busted orb and energy gate) you can leave the level if you want. You are, of course, still required to beat him to proceed with the rest of the game.
