First awesome work and I'm sorry for the loss of your loved one.
I don't see a reason to limit troops we can deploy, if the aircraft can fit 12 then fit 12, some missions should have 4 or 6 aliens and some should have 30. If the player doesn't want to bring more troops then they shouldn't, but don't make the aircraft seating unrealistic because some don't like it. Maybe make the beginning aircraft a short-range helicopter and let us work our way up to affording a ch-53 or ch-47.