Squads are already planned to level up as a whole, but just SpecOps. SpecOps squads are meant to be your bread and butter, while military squads really cover less important things. If you were to compare it to X-Com UFO Defense, all the soldiers you'd have in the game are SpecOps soldiers in this. Military squads are basically you taking control of soldiers from the nation's military, instead of the "nation's best" selected for the SpecOps squads.
And as for trade routes/food supply/civilian impact[/naval units], I'll just design some systems for that.
For civilians, this is what I can think of at a glance:
-Lower food = Dead civilians
-Bombed cities = Dead civilians
-Successful invasions = Dead civilians, military infrastructure
-Dying civilians in your nation = lower funding
-Dying civilians in other nations = Eventual conquering by aliens, increased world panic level if done
A bit unsure about further impacts, because lower funding and alien occupying (read: killing everyone and building on the ashes) seems to be a bit low of an impact.
As for trade routes and civilian resource gathering, don't really know where to go on that. Maybe more resources/trade routes = Discount on items related to the harvested/traded resource, and vice versa? If the aliens decide to drop a bunch of battleships/whatever in a trade route to another nation for ammunition, then ammunition prices would skyrocket, and so on.
EDIT: Keep in mind I'm trying to keep it generally abstract enough so I don't need to keep a list of every trade route and resource collection spot ever and constantly update it.