I'm not at all averse to seeing the engineers in the game, in some capacity. I don't like the idea of them being a big stomping enemy that you have to gun down though, even as a boss. I'd much prefer we just pick through the ancient remains of their structures or, at most, have them as background antagonists.
I love the way they were presented in Prometheus (despite serious reservations with the film as a whole), and that was largely due to their aloof, eerie presentation. Shooting them in the face rather diminishes that feeling.