I think there was consensus over the intel rooms last night in preference to the original design. I think you could do a good combo of both, though. Have your current sinister desk and vault, but behind the desk is overlooking the NASA room (as many put it).
I think we proved pretty adamantly that a pair of engineers (or even just one, probably) can effectively control that room as is (that is until they get bored of camping out). As I suggested in game a ceiling drop would be very useful in getting those campers out. A demoman could drop down some pellets of doom and flush them out. The room was too small for a single spy to really take anything out if an engineer was still hiding out there.
I’m really curious about the spawn problems that plague. You’ve got more than enough locations so that shouldn’t be the issue. I’ve found that if you’re short spawn locations for a player on one team, TF will put him onto the other team, regardless of which team it was set to be a spawn for.
Here’s a suggestion, use the entity report menu option to bring up a list of every entity, filter it down to info_playerteamspawn and select them, entire teams at a time and set them to the appropriate team. Hoping that made sense, I have some reports to write (and it’s only been the first class too).