I personally think the 'only one' element of improvements needs to be more rigourously enforced. Tricking your way around it is just lame, and means we can all leave enemy planets alone until they build something we want to steal to twink our way out of the game. If you can have more than one, let a successful non-military player just build them like regular people. If not, then stop people spoilting the checks.
Simply deciding that you get 'one' of all these omega and hyperion structures, and additionals cost an assload of money. would be a fix. Might as well let everyone build as many as they want, if they've got the resources.