1. When a Sim has a low Fun score, they pretty much never choose to use the item that will raise their score most quickly. Sure, I guess that's where the player comes in, but it's still annoying that they'll always try to play the Myshuno game instead of just watching TV, even though they'll usually stop the former without really raising their score that much.
2. Sims having the same Wants over and over and over again. I like to use the Wants as a guideline for what to do (which I guess is exactly what I'm supposed to do), but it's annoying when all they want to do is tell jokes to someone else. This is sometimes even the case with the Money aspiration. A Sim will want to buy about 800 living chairs, even though hardly anyone ever uses them. Some of the Wants are pretty ridiculous anyway, like when the family-oriented Sims desire to have ten kids (come on, does anyone really WANT to have ten kids, or do they just end up with that many because they believe in sex but not birth control?), but at least that's something to work towards.
3. The great disparity in the Sims' life goals. Most of them just want to reach the top of a particular career path, which is time-consuming but relatively easy. But then you'll get others who want to own five top-level businesses. I have Open for Business (they probably wouldn't ever have this goal otherwise), but I haven't actually tried running a business yet. It sounds a lot harder than most of the other goals, though.
4. Those phone calls where someone just says, "Hey, how come we never talk anymore?" Hey, if you're so desperate to talk, why don't you just do it, instead of making me call you back again? Even more annoying is that I sometimes have a Sim try to call that person back, only to find out they're at work. They'll also call at all times of night, even though they get mad if your active Sims call them at late hours. And hey, why aren't there any more calls saying you've won money or asking if you canoe, like in the original Sims?
5. I find getting Sims through college to be a bit tedious. It's not that it's all that difficult, just that it takes a long time, and mostly just consists of making them do assignments constantly. Is there any way to make Sim university life more fun?
6. Even if multiple Sims are hungry, each one will often just get food for himself or herself. I usually stop them when I notice it, but if you don't cancel the action in time, they'll usually have already lowered the food supply.
7. There's some bug in my game that has, in two houses, resulted in stoves from which I can't remove the burnt food, and because the food is still there, I can't sell the stove. At one such house, I ended up building a shed so the useless stove would be out of the way. Has anyone else who's played the game had this problem? Maybe there's a patch for it or something.
8. If there's a fire, the Sims will all run right up to it. I know I've mentioned this one a few times, but it's just so baffling that it's worth mentioning again.
9. The fact that I can't switch back and forth from my game window to do something else on the computer. I could with the original Sims (it was kind of slow, but possible), so what gives? If I change windows and then try to get back to my game, I just get an hourglass against a blue screen. Today, when I was playing, the computer switched to another window by itself (it used to always do this to alert me that my virus scanner was updated, but I've since learned to disable that when starting the game), so I lost everything I'd done in the house I was playing since my last save. Fortunately, it wasn't that much, but it was irritating nonetheless.