I think the innovation Greg is referring to, is that this type of base hasn't been done in this way before. And I totally agree with what they are trying to achieve with it. But so far I'm not personally a fan of the side view.
From a gameplay view, side vs top is only aesthetic. And a 3D-grid would just add complication with little gain.
Having the base underground limits the design I think. The dream would be the same concept in isometric view... like SimCity or Apocalypse city layer. But that is an ENORMOUS effort for a small part of the game.
I love this pixelart image by Sohei:
http://fc02.deviantart.net/fs20/f/20..._by_iSohei.png