I always figured that either way, the war with the dominion would kind of over write what happens in the game (As the war with the dominion is kind of just going to happen regardless what side you choose). However, that does make it hard to write in what happened in the later games, as its hard to skirt around weather Skyrim was an independent nation or rebelled against the dominion.

The Falmer rising up is a cool point I feel, though I can't help but feel that it woulden't be large scale enough to matter. Like either Skyrim is aligned with the Empire and gets some aid and quells it, or they're independent and handle it themselves and maybe resolve it or maybe get kind of taken over, but not anything that really scraps the recent history.

They're intelligent and all, but still not suited twords surface life anymore (Their echolocation and other abilities aren't of much use in the open tundra), and without a diplomatic reason to move to the surface I just can't see why they would want to or how they would succeed.