Shouldn't be hard to top the old design in that department.
Aside from that, the facility needs lots of office space and the latest utilities and the head of OBL on a pike at the main entrance.
I think you're ABSOLUTELY right, this is one big reason for no satisfaction in these designs. Everything else looks relatively pathetic. Sadly, and yet understandably on so many levels, what may stop this from happening is fear. How would you answer the concerns that it would be a total target for future attacks and that people would be afraid to work in them? Maybe the idea mentioned above about them being "hollow" or not inhabited above certain floors except for the observation deck is a really good one.