Welcome to the game!
A brief look around the forums will tell you that many people agree with you on the mothership thing - which is good, because if lots of people want it, I'm sure Muse will work on it. They're pretty active on the forums. In fact I'm sure they already are working on it, since I've heard rumors the new "Adventure Mode" will have mothership type missions. The boarding aspect, however, has been definitively rejected. The problem is that it's completely different from the idea of the game, which is ship vs. ship combat. And, like you said, there are other games you can play for that.