When stealing a aircraft, clear the map of bad guys first. Otherwise as soon as you claim it, they all turn around and shoot it! How weird is that, it’s their plane and rather than trying to take you out they destroy it.
Build more bases, more planes, more teams. The game give next base location, discover it, exploit it, equip it and it opens new area to explore. Do that before find a new base will be troubles, find new base is just have some basic knowledge of geography and a bit of persistence.
EDIT:
And don’t let many lairs, if you can’t do anything against factions wars, at least you have some controls for enemies attacks.
I think I had a bad start. I didn’t discover any other bases until late in game. I concentrated on tech so as to be able to handle the Sirens and my resources were always low. I stole a ship making a total of 2 which isn’t now enough to handle all of the threats. To make things worse my troops are always needing rest.
I am now in this vicious circle of heal protect heaven, heal, protect heaven, and I don’t seem to be able to get out of it.
It’s becoming more and more clear to me that you have to know the game inside out to triumph, and don’t play when your half asleep. 
You also have to save scum, and take a “leave no man behind” approach, unlike past XCOM-like games where squad member deaths was a part of it all.