Yeah, the first one def. had some problems.
The main one for me is how they used time as a resource. Like thexor mentioned, you could just outwait any heat. You also had to wait to replenish your minion stock (Or you could pay money to replenish them). I mean, it was really cool how you basically had an infinite source of minions, but I found myself just waiting until I got a full amount again. Plus training took forever, so often it's best to leave the computer running for half an hour (Or more) while everything replenishes. Time is used in RTS's to force the player to plan ahead. In starcraft, if you could build anything instantly you would simply be able to react to whatever your opponent threw at you. Time should be used to force the player to plan, not as a punishment or form of resource. Instead of training minions up, maybe you build a special room that supports X number of special minions, or something, that cost infamy to build. There are a ton of possibilities.
Another thing is heat. Heat shouldn't go down passively, it should be managed by the player. This makes it from "Wait for it to go away" to "Okay this mission would cause a lot of heat I better make sure I am ready to counter that", or something. Maybe. It does need fixing.
And yeah, tourists.
Personally I liked the traps, IF you could set minions patrol zones or no-go zones. The security camera system was pretty cool, I think that should be expanded. This area is off limits to any outsiders, anyone that enters this area gets X'ed (killed, captured, confused). This area is off limits to minions, so hopefully agents will fall for it. Minions should also be able to dodge certain traps, or something.