A Few Ideas....
Firstly, I really think this will be a good game when you finish it.
A few suggestions, since you seem to want them. :)
Instead of safely crash landing on the base every time, why not have the hovering circle over the base as well? Then you have to use [BACK] to safely dock every time, unless you're just dropping off cows, in which case you can just hit and run it? You could make [D] the dock button (available any time you're in the base circle, but you'll still crash / move if you didn't hit the brakes), from where you can do all your shopping, upgrading, cow laundering, etc. [S] is fine and all, but d sounds more intuitive. :P
Right now, [BACK] is sort of a vertical brake - you can still move left and right (per momentum) but you stop falling and rising. Not sure if this is intentional, but neat effect.
Possibly you could use upgrade trees? For practically everything? Ex:
Brake Lvl 1 (Default): "Vertical Inhibitor" - "This item causes you to stop falling and rising, a basic requirement for docking, cownapping, and more! Uses 5 fuel / second." NO_RISE NO_FALL
Brake Lvl 2 (Costs): "Momentum Decelerator" - "This upgrade to your brakes causes your ship to rapidly slow down, possibly avoiding that unexpected tree that just always keeps popping up. Uses 4 fuel / second" NO_RISE NO_FALL HALF_ACEL DOUB_DECEL
Brake Lvl 3 (Costs): "Rotational Lock" - "This upgrade causes your ship's brakes to match the exact rotation speed of the Earth, instantly stopping your ship no matter how fast it was going. UFOWares offers no cattle insurance in the event that the stop proves too quick for them to handle. Uses 3 fuel / second" NO_MOVE
I can think of several others - fuel tank upgrades (100u, 125u, 200u, etc.) weapons upgrades, etc.
Also, depending on how combat works out, the aforementioned brakes could actually prove useful in aircraft - vs - UFO combat. Imagine, if you will, you are going 200 mph, with six fighters trailing you at 300 mph. They're going to catch up eventually. But, look, a cliff with a very small opening... shall we play chicken? So you zoom towards the ridiculously small hole, the aircrafts follow you at top speed, you get closer... closer... no turning back down... hit eject, it's impossible!... then you swerve up and slam on the brakes. That, my friends, is six dead airplanes.
Since the UFO is alien, it makes sense that it can rise and fall at will. But human craft, at least with the exception of helicopters, fly by generating speed and then tilting at an angle to rise (flying) or fall (diving.) I think it'd make the game more realistic (and strategic) for the human resources to be crippled in this way. Imagine staying a mile above the frustrated human who can't generate enough speed to chase you down (since a straight vertical rise = stalling out, aka crashing.) I dropped the bomb! :D
Please feel free to message me if you'd like more ideas on this game, I could sit down and write my heart out about all the things / upgrades I could see in the game.
God speed and good luck!