I have two simple feature requests:
1) Keyboard Shortcuts
It would be good if there were keyboard shortcuts for everything, so we could place our units and do other actions faster.
For example: CTRL+U to display the units, CTRL+F to display fleets, CTRL+S to add subs, etc.
2) Click-and-drag Unit Selection
It would also be cool if you could click-and-drag boxes around units (even from different fleets) to select them for movement, like most other RTS games.
That's all
Implement these two features and you have the best game on earth. Forget all that other crap about different kinds of units, radiation sickness, etc. The simplicity of the game is what makes it so awesome.