I spent some time playing today, here's my feedback:
* Long load time, seems frozen.
* Do something at start rather than dump the user on the full menu. Jump them right into playing.
* Use icons on the menu buttons. It currently looks quite like a "developer art" game, even though it isn't. Your fonts are very nice.

* Separate icons a bit. Mission/skirmish, units/research/perks, options/help. Applies to all screens, eg mission screen: return, research/units, don't need add credits in this screen, help.
* On mission end its a bit confusing that I have to leave the mission manually. Maybe because the Continue button makes me think it's what I want to do -- I won, now I continue to the next thing. Need better button labels.
* Sometimes the mission buttons look grayed out. Something odd there.
* Unit modify screen, should be called "configure" maybe, the replace/sell buttons were confusing. Took a while to figure out replace is how I put something in the slot, even if it is empty! Select box selected drawable needs more padding on the left. Help button on this screen says "test help". "Credits" label isn't centered.

* Give the user a reasonable zoom when a mission starts. It leaves me wherever I was!
* Use double click for something, like deselect? Auto zoom?
* Use two finger tap to box select. It won't trigger zoom because the touches never pan. This will make selection waaay better.
* Pinch zoom should zoom to the pinch location (halfway between the initial pointers), not just the screen center.
* Pinch zoom sensitive is odd. When I move my fingers, they should stay in the same world position, the world just gets bigger or smaller. It makes a big difference.
* Panning sensitivity is off. Zoomed way out, I can pan the whole map with a tiny movement. Zoomed way in I can pan all day and get nowhere. Like pinch zoom, when I pan my finger should stay in the same world position.
* Can get rid of the end button by making a pause dialog. Stick pause in the corner.
* Maybe nice to hide the help and +/- buttons.
* Could disable buttons that can't be pressed, eg Buy Unit.
* A unit with just a shield runs away when part of a group and told to attack. It should take a defensive role and follow one of the attacking units.
* Showing how many missions there are may increase the value of paying. As it is, I'm on mission 13 but have no idea if its worth buying. If I'm on the last mission, probably not.
* Make a turn-based multiplayer mode! You don't need a persistent server connection, so you can use standard technologies. Eg, you could run a servlet with Voledmort and probably server a huge number of players with a Linode (my
referral link 
). Both players take turns, then the simulate runs for X seconds. Maybe if no one is in range it runs for longer, especially at the map start. It'd be awesome! You may need some way to balance it though, eg a max expenditure, no perks applied, etc.
* Mission select has research and units, but no perks? I didn't see perks until later when I went back to the menu.
* This is a bit of a trick, but it works: have a free credits button or dialog which shows a dialog saying "rate 5 stars in the app store for X free credits!" and open your app store page. 99% of users will do it, even though you have absolutely no way of validating they actually rated you. Don't do this right off the bat, only give them the option once they have played for a while, like level 10, because credits don't mean anything to them yet. Maybe wait until they have reconfigured their units at least once and then played at least one mission.
* Gameplay is quite neat, I look forward to seeing more. You may be able to do more micromanagement stuff, eg a bomb you have to click that does an area of effect, or special weapons that have a cooldown and have to be used manually (similar to WoW abilities).
* Moar missiles and explosions!
Your game is really awesome, I hope you stick with it! It is fun already, but has tons of potential.