I have not played this game in a long time, at least not in any way that involves paying attention to storylines that are not modded, but based on what I remember, not choosing a side is the worst option. The civil war was instigated by the aldmeri(?) dominion to put skyrim into chaos and keep them from pushing the elves back out while they silently take over the empire. It makes things slightly better, but I still didn't like how terrible both sides were.