In addition to having a much larger viewing window and superior light transmission for passive "view through" use, the EOTech also has a "viewing window" that's wider than it is long, which, at least to me, seems to make it easier to aign all the different optical axes--in order to use an RDS through NODs, you need to align your eye with the tube, then the tube with the optic, with a "tube style" or any longer optic, you also need to align your eye and tube to the tube of the optic, versus the "window" of the EOTech. The EOTech's design and technology make it function (at least to me), much more similarly to a HUD than a projected dot...probably because the EOTech essentially uses HUD technology--this of course comes with much higher power consumption, and of course, with a much more complicated technology, there's more room for things to go wrong.
The other feature I like about the EOTech is the "NV" button, meaning a near instantaneous switch between NV and visible sight pictures, rather than having to crank a brightness dial back and forth, and hoping you land on the right setting.
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When I was playing with that setup I found that the T2 was surprisingly on par with the large window of the eotech. I already had the T2 and used a friends eotech Exps to experiment. When using it without vision, I found the T2 a little easier to get into. My theory is the smaller window helped since I was not used to it sitting so high and would find myself getting lost with the larger window of the Eotech. This is purely my experience in the short time that I compared the two side by side.
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You mentioned it yourself, but I would suggest that this more of a familiarity issue than something that is natural to the two optics.
Not only do you own the Aimpoint (and therefore use it more often), but you were also experimenting with higher positioning, meaning that you have not necessarily developed your NPOA using taller optics. As you mentioned, it sounds like you're indexing off of the optic's housing itself, then looking for the aiming point within it, rather than staying focused on the target, and letting the aiming point simply "appear" in your field of view.
Standard disclaimer:
I continue to own and use both Aimpoint and EOTech, and have always felt that they both have their own pros and cons (big con is that it's a little hard to get an EOTech mounted on a Glock compared to a T1
), but for this specific application on a long gun, IMHO, the EOTech is superior.
~Augee