OK, I'm not going to go in to HEAVY detail on the game here, because honestly Blackdrazon covers more, better than I could have.
There is something he doesn't go in to:
Controls.
First, the controls of the game are not the most intuitive. This is forgivable, just annoying to get used to though.
The real problem is the tactical control, or.. lack there of.
Unless you tag them, enemy agents can walk right in to your base, without alarms raised, minions freaking, etc. (Well, you'll get an alert that your security door was bypassed), they won't even do anything when the agents start shooting your equipment. There is also no way to automatically set enemy agents to hostile.
Also, I don't know about you, but if I were an evil genius and had a base like that, I would have a very detailed defensive plan, that when the alarm sounded, everyone knew where they belonged and what they needed to be doing.
Instead, if you put it on high alert, sometimes your minions will run out of your base after foes.. one at a time, and get picked off.
There are several other significant flaws, but many of them are fixed in various patches, or by simple mods.
Over all, it's well worth playing. Just don't expect epic win.