1. The "make a mess" feature. No matter what, all toddlers and children will do it if they are left on autonomy for virtual seconds. It doesn't matter if the parent disciplines them, if the child is neat or has the responsible trait or if the toddler is angelic, they will all still make a mess. WHY?
2. The mourning/grief system. As has already been mentioned, I also hate that toddlers get the 2-day sad moodlet over a Sim they've never met. Since they are only toddlers for 8 days, they are literally sad for 1/4 of that life stage per death and there isn't really anything the player can do to improve their mood. At least with children and older Sims you can give them a moodlet solver.
3. My biggest annoyance, though, is the situational outfits and horrible randomly generated seasonal outfits. This could be improved enormously with a fix that removes accessories from random outfits. Also, why do random pajama outfits often have glasses? Who sleeps in their glasses?