Yes, that is the problem. There are so few pilots that I find it better to have them in fighters. Most of the game you are left with three pilots. And then when returning from Precursor system you lose two pilots. So if there are more, I would also put one to the MS.
BTW does anyone knows why Joseph joins you? Just to tell you which system to go, help you shoot a few aliens and then run away with all equipment you gave him? Can it be changed so he stays?
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