Well, as far as origins go.. I am not so readily shooting down people's ideas.. so here is my concept for a MS....
In the TV show.. which is where I get a lot of my ideas to transcribe to this game...the motherships are.. primarily, even by the Goa'uld.. only used to influence a ground assault beyond propaganda in very dire circumstances. In fact the wraith are the only race that use them to assault on the ground extensively enough to warrant an in-game counter part to do so.
As such, the main role of motherships, have always been to facilitate movement, transport etc etc... they only fight each other in space on a regular basis.
Assuming (this is, just assuming..) we ever got planets. they would act as extra planetary defences, you would have to allocate your mothership to a system (more on that LATER! lol...
), for it to protect.
On another point.. perhaps you can upgrade your mothership to facilitate your troops with their stash. Perhaps purchase the mothership, and update its capacity and beaming technology. This add's... %steal to your naq hits, which is we reduce the %taken from hits again.. would add another feature to the game to play with. At the same time, whenever players engage in battle, the motherships CAN fight.. and this capacity CAN be lost... and then add in a similar system of mothership attack/defence/hangars to the fight details (but obviously, they still have no effect on the ground battles except for increasing the % steal).
However.. you should have it that, if your mothership is reduced to 0% capacity, you lose it and have to rebuild it and lose the naq taken. Make the mothership pretty disgustingly expensive, and then capp how big they can get. No mothership in SG-1/SGA was ever untouchable or had no achillies heel.
Could also.. throw some race specials out there... Asgard Motherships are pretty good all rounders, but cost more to upgrade capacity wise. Goa'uld are weaker than asgard, but have reduced capacity cost. Replicators have higher MS attack, whilst Tauri can be upgraded to have higher strike or defence.. make them flexible. I don't think Tok'ra's should get MS's, they have enough benefits as it is.
Some food for thought to answer the complaints in another thread anyway ....