I think you missed the point with the mothership instructions, or else I did. You fill every space on the tile once the mothership is revealed, and continue to refill it as long as there are spaces. In other words, once the mothership arrives, it's endgame - they start coming faster and are ready to defend the objective. It actually makes for a pretty tense last few moves, as if you reveal it late you're racing the clock to get there through the martian hordes before they run out (co-op mode).
Maybe you're right and I'm wrong, but that's how I read it and played it.
We initially read it this way. We agreed that it made the game more tense. There is another thread around here in which Todd, the creator, says that it works the less climactic way. I'll stick to your way, more fun IMHO.