I see. Perhaps this could be fixed at some point in development, otherwise it might force the player into a playing style they don't want (having dropships at every base).
I can think of these ideas off the top of my head for a fix:
1) If a base is attacked that has soldiers and gear but no ships, before going into the combat phase have the soldier equip screen come up automatically and then have combat (this would actually be like the original X-COM/UFO game).
2) Move the soldier equip button to the main base view menu, doing some re-vamping (I'm guessing this might take more coding work, and possibly create some tedious programming headaches).
3) Have all bases set up by default to have a "ship" that is really base defense stations (could also be called "base patrol" or "guard posts" or something else) that soldiers can be assigned to along with equipment for the purpose of defending a base.
Personally I don't favor the second idea, and although the first of these three would be the most like the original game, I think the third would be kinda cool given the freedom it would give to the player for their playing style, making it my personal favorite solution of these three.
Of course there are probably other possible fixes, these three are just the ones that popped into my head right away.