A definitely nice find. I've been reading around a bit and I see you are planning on touching on a few problems. Just wanted to voice some issues myself.
What exactly is money good for? Or employees? Ever think about giving zones "upgrades" to their stability with the use of money, or that employees could work out the crinkles in the system?
I also saw that you thought about doing two different modes of "starting." Hopefully when starting from scratch money will be a much bigger issue, such as starting off with fewer classes and enemies that you can later "buy" as an add on (like an expansion).
One thing that has really got me scratching my head is how you can build zones instantly. Ever thought about it being a "process" where the time it takes to build a zone is relevant to the number of employees you have (plus how strained they are with other things)?
I saw that you also planned on adding barriers. Thank you! I have five different starter areas with five different progressive areas that my players can go to, but they all seem to end up at three of them, so those zones are ALWAYS being stressed out. Would definitely like to refine it so the players can't cross over to zones.
Last thing I'd like to mention; XP scaling much? Existing players seem to hit the cap within a day or so.
Anyways, hopefully you expand more on options as far as designing and business goes. Can't wait to see the results!