I think the root of the problem is the hexagonal nature of the structure. Perhaps you could make the gatehouse a wall upgrade like in 0 ad, then you can require that it be placed on a straight section, which should make it easier to design visually.
I think I could improve the gatehouse by changing some of the logic of how units move through buildings. When a unit enters the gatehouse, the individuals could bunch up to enter "single file", which would allow me to shrink the door without having people seem to phase through the wall.
Anything like that, though, would be post 2.0.