Common annoyance in the early game:
You have two bases, with all their hangers full and no free hangers elsewhere, and want to swap two vehicles between bases.
Currently, you can't do this without a third hanger.
What I suggest allowing is the following:
If you order a vehicle to travel to a base via the map and push the "ship" button, and there's no room for it but there are hangers in use, the game gives you the option to pick a vehicle you want to swap with.
(As part of this, it checks to make sure there will be enough space for each vehicle and its contents at its base after the swap, and rejects it if this check fails.)
If everything is ok and the old vehicle is in its hanger, it takes off towards its new base. If it's already in the air then it just gets its home base reassigned.