Those are excellent points.
In fact, I think perhaps there should be an element of AI assistance when building a base - the computer could "suggest" spots to lay down stuff to you (with translucent "ghosts" or some such) which you could follow as a newbie, or ignore if you (like I) relish the challenge of base invasions (they're so rare...)
As another aside, I've always thought that the basemaps should have equipment accessible to the player on the map, eg an armoury or lockers in the living quarters that your crew can get more stuff from - after all this is their homeground... it'd be nice to grab more ammo, or maybe pick up a more kick ass weapon or something - like you would in real life if your base is under assault