Okay, just from reading the description and a few things that have to be researched, I can already suggest a few improvements to fill a few plot holes. First off, since the shelter was designed for VIPs and government types, aka the types who absolutely NEED their creature comforts with as little (read: none) hassle as possible, most of the tech I have read about (water purifier, water pump, greenhouse) would already be there. Make it so that the damn things broke or something, so you need to research them in order to fix them. Unless of course this particular bunker was never finished.
Just a note from someone who literally just read the description, read a few comments, then downloaded the game. I saw what looked like a glaring plot hole and offered a suggestion to fix it. If it is explained in game why this bunker is so bare bones in spite of its proposed lazy population of professional paper pushers and toy dog petters, then feel free to ignore this comment.