Well...here is how I see it.
Price? EOtech. Aimpoint becomes more expensive because it requires a decent mount. Some say the EOtech does also. If you consider mount + optic together as a system when formulating price, in most cases EOtech will be cheaper.
Red dot? Either. This is pure preference. The Aimpoints' is more simple being a dot. The EOtechs is more busy, however you get a big circle for up close really fast, and a tiny dot for long shots. Aimpoint is 4moa, and that is good enough for COM out to 2x the 556's frag range anyhow.
Battery life? Aimpoint. New gen 3's with 50,000 hours of life on a setting of 7 out of 10 is very impressive. Gen 2 was still better than an EOtech with AA lithiums.
Durability? Jury is still officially out. However, Aimpoint gets a lot more weight because they've been A] approved by the military B] been around a lot longer.
Weight? Aimpoint is lighter, but depending on mount...that can change. EO's vary between N and AA battery models. (obviously)
Field of view? This is subjective, but most reasonable people would say EOtech gives greater FOV.
Warranty? Aimpoint. 10 years vs. 2 years for the EOtech. (note that Aimpoint is also 2 years for professional or competition use)
Waterproof? Aimpoint military models. EOtech says 33ft. M series Aimpoints are 75ft + (who scuba dives with a red dot besides SEALs?) Comp C's and the civilian/hunting models of Aimpoint are 17'. This category is moot for 99.999% of folks.
I've got an Aimpoint. I liked the warranty, battery life, and simple dot better, and these were the key factors. Although I think the EOtech's holographic concept is pretty neat, I just want a simple spot of a dot. I want as little distraction as possible and don't like busy reticles unless they are range finding ones for bench guns. Also, mounting options were better for use with co-witnessing iron sights. The EOtech requires a riser mount to do lower-1/3 co-witness and that negates the cost saving integral mount of the EOtech.
I did not overlook the EOtech over any fears or doubts of reliablity or toughness. That was not considered, as both optics are clearly proven in my opinion. AA battery option was very, very tempting though....
Personal preference. Best advice (aside from buying both) is to look through both and handle both. That will help you a lot.