Personally, I like the Empire for a couple of reasons.
First, I hadn't seen any elves at all in the Stormcloak army. I might have missed them or something, but I never saw any. I've seen at least 2 Dark Elf Legates, which is an officer level rank within the Imperial Military.
Second, I agree with the Thalmor. Talos was never, and should ever, have been a god because he was a normal man. He was just really good at what he did, and knew what had to be done. It's a religious argument anyway, which would be devolved into throwing poo at one another. In the end though, I believe the Thalmor to be correct.
Third, there seems to be a racist undercurrent to all Nords in Skyrim over the Elves. It stems from when Ysgramor killed a very large sum of said races populace, which was in defense of being attacked in an unprovoked way by those Elves. The Dominion, I believe, decided it was time to get some payback, and the best way to do it was to eliminate a false deity (that is my opinion).
At the start of the game, whenever I play an Elf, I side with the empire. I think to myself, well I'm in this situation because I was in the the wrong place at the wrong time, with the wrong crowd of people. Basically, my characters did nothing wrong, but could be seen as consorting with the rebels, and therefore should be executed with them. They are only doing their job, if I were in charge of an Empire that had rebels, I'd do the same exact thing.
Anyway, I feel the Empire is best suited for my Dark Elf characters simply because of the above reasons. I simply do not like that there is not one single Dark Elf officer within the Stormcloak ranks. Dunmer look cool in Imperial heavy armor anyway
