Could I suggest a starting option that instead of getting a default base when you start the new game, you use the same screen when building the 2nd, 3rd, 4th bases etc. and just get to place the access facility, then you have to build and buy all your stuff.
That way you could really set out the base the way you wanted.
I was also thinking, is it worth holding off aliens for the first month so your score doesn't plummit, but then, if this happened in real life, you wouldn't get a "Hello, we're about to invade, would you like to prepare". So you could maybe have that as an option too.
Just a thought