Spacebase DF-9 is looking damned good for an Alpha (currently alpha 2), and already has a lot of features with a lot more on the way, apparently. Obviously it's a bit buggy at the moment (the AI & path finding are crap), but DoubleFine seem to have something really good going on with this, and of course they know how to make decent games, so the finished thing has a good chance of being really awesome.
It's similar to the isometric Bullfrog classics (Theme Hospital/Dungeon Keeper) while being unique in its own way, so worth a try if you liked them back in the day (especially if you have the 20% off discount for owning a previous DF game, otherwise it may be a bit pricey for what it is, IMO).