upper tower is far too overpowered like you identified.
An egg with two acid tubes are basically invincible when they are behind the grate thing as the only way to get up is jetpack, but you wont be able too with the tubes, and you'd have to shoot quite a couple of times to disable the tubes to allow you to jet up to the egg, which is far too powerful. You should nobuild it.
apart from that smexy. The lights are great, and the new base layout is very good.