This sounds kind of similar to a browser based MMORTS like travian and the million others that are out there but maybe in a real time/non browser based form?
If the city building side isn't influenced by combat how do you win? What happens when you win the battle that your squad gets sent to? What is the "end game" of it all? Is this all going to be multiplayer or singleplayer against AI? Is your city going to be persistent like an MMO, something that will be built up over extended periods of time, or will the game function like a traditional RTS with new matches beginning and ending in each play session?
Not trying to criticize your idea, it sounds cool, but it would help to answer those questions I think so we can get a better idea of what the concept is.