Not "favorite" per se, but an old, obscure game with a lot of problems that I still love: Evil Genius.
Now it's a 100% accurate movie villain simulator, so obviously you can't do anything yourself (except gloat over your captured foes). Instead, you give your minions orders. Thing is, the minion AI could be charitably described as abysmal - minions will often stand next to a fire and decide to go get the fire extinguisher 2 corridors over instead of the one right next to them.
Some might say that this is part of the flavor - you wouldn't be a real evil genius if your minions weren't as thick as a cartload of bricks, right? Thing is, even when it works right, it is sloooow. Everything in the game has an animation. Minions leaving the island to go to the world map. World map minions bringing back loot. Minions building. Minions repairing things. Science (more on this later). Everything takes a while. And eventually, you get tired of waiting.
Room and Item descriptions are usually incomplete at best, too. The game itself only gives you a rough idea of what you're supposed to do - you pretty much have to figure out the how. I've played this game twice over and I still need to have the Evil Genius wiki open just to make sure I don't f**k up. (Big props to the wiki guys though; that thing is a lifesaver!)
Special mention goes to the science & research system. Basically in order to unlock new item blueprints, you need to combine an existing blueprint selected by your scientists (which is slow and, worst of all, random) with 1 to 3 lab room experiments. The game doesn't outright tell you which three though, not without you spending thousands upon thousands of dollars bribing the researchers not to waste your time (not even making this up. this is the canon reason: your researchers love to research for the hell of it and will waste your time given the chance). Thankfully, one of the three Evil Genius avatars, the Blofeld/Napoleon expy, reduces the cost of that bribe by 90%...or would, if his ability wasn't bugged. (Again, big thanks to the wiki here - they have ALL the research paths!)
Finally, there are your nemeses: the Super Agents! Each one of them armed with unique abilities to infiltrate your base, and 3 of them - a Bruce Lee clone, a Rambo clone and, obviously, a James Bond clone - are absolute TERRORS. Bruce can basically one shot any minion in melee, and minions with guns don't shoot enemies in melee range; they engage them in melee combat -_- Rambo dual wields M60s...need I say more? And James Bond randomly causes explosions around your base. If it wasn't for a handy glitch that allows you to permanently pacify them until they can be defeated permanently, they'd make the game almost unplayable.
I could go on, but I think that's enough. I still love the game despite all its flaws. Besides, you can execute random minions anytime they get on your nerves. And what more can you ask for from an Evil Genius simulator?