Comission is too much profit for too little effort. You may fight vs other peaceful factions, because your faction declared war? Who cares? You dont get any direct orders, you may go explore the border of the map and still get extra money. Lol, faction war, in fact, is positive side, not drawback, because you get legit reason to raid their colonies.
Also, it is too easy to get a capital ship, having comission, but pretty hard to get one without it.
What i suggest:
- system of direct orders. Sometimes they give you special order, and you must obey, because they count on your forces, and if you will not, it will be a huge hit for their strategic position. So, you will have to pay compensation for the losses. And will be kicked off if you dont. Also big rep penalty with that faction and low penalty with others (because they see that you are not reliable man).
- if you complete several special tasks, they will give you an opportunity to buy capital ship (maybe at big discount).
I mean: the description of some capitals says that it is a masterpiece, and it is pretty expensive. Why would they give em like candies for everybody?