I cast myself in Shepard's role rather than stooping to his written level of intellect. Honestly I don't see anything about the Reapers as being difficult to understand, though Shepard probably does. I'm not a very good role-player.
I'm not really talking about shepard. But I think sovereign was pretty convincing within ME1. He was so confident and indifferent, I loved it.
Just think about it, you're dropped in a world, where you're using technology you don't understand, for living, for fighting, for everything. Then suddently you happen to bump into one of the guys that made all this up, and to you realize they're gardening organics just like you would treat your back yard.
Everything from the music to the main missions being a foreshadowing of the main plot make this possible.
I don't blame you for getting invested though, some things are too subtle for people to grasp and Lovecraftian horror is 100% around subtlety. Even if you don't buy it you're facing a kick ass villain whos defeat gives you immense satisfaction. A win-win scenario 