Ultimately, I think this is something that comes down to personal preference. You're going to find you either like one or the other more.
However, I will take a stab at briefly listing the plusses and minuses of each - with a brief disclaimer, I own both, but bought each of them a while ago, so there may be newer models with different/better features.
Aimpoint plusses - a little more rugged than Eotech. Longer battery life.
Eotech plusses - cheaper. I personally find the reticle design allows for faster target acquisition at CQB distances. (But others may find the exact opposite).