I didn't get a chance to test the layouts yet but here are my overall impressions (I should note, I was testing this on a xoom w/3.1)
I'm not sure how ports work but it seems you have built in interface that just interprets what the touches mean on the screen for the game (which is run separately?)
By far the best interface would be the touch one (where it clicks where you press) but since the game is designed for a computer screen, all the buttons are too small and difficult to press (especially the arrows on text fields). Not to mention some text fields (aircraft stats), leave out ONE stat (making you have to scroll down to see accuracy). Ideally the interface should be less cluttered so all the stats would be available.
I ended up using the laptop method and a 2nd finger to activate a click (right click disabled) but it got very tiring holding my hand up there.
I have attached pictures to show you what I mean about the text. It isn't a size issue, its a pixelation issue.
To be honest, this could be an EPIC game for a tablet. Its perfect for touch based input but it really needs to have a totally redesigned GUI. For example, on the bases page, using Honeycomb fragments, you could have the list (aircraft, research, production) on the left with the map on the right, then when you click a on research, it would remove the map and replace it with a research interface, leaving the lists up on the left so you could select a different area after you are done with research. ALL buttons need to be larger for touch based input and the whole interface needs to be simplified (not in content but in accessibility since you don't have a mouse and keyboard). Again, i have no idea how this port works and if this is even possible to implement...
That being said, if you intend to continue this project, I highly suggest you limit it on the market to tablets only initially. Once that is working well you could reduce it for smaller devices. Going from a computer w/multiple inputs is hard enough going down to a tablet, not to mention even smaller for a phone
Oh, also, it freezes up in the campaign mode when trying to play your first battle. It goes to the black screen, music keeps playing but nothing happens.