With autonomy off, I can still control my Sims (just pause and queue up tasks), but one thing that annoys me is that they will stop doing tasks if their fun bar maxes out. (For example, if I want them to read to increase a skill, I want them to continue reading even after the 'fun' bar is maxed.)
As noted by another poster, if needs are getting crucial, they'll cancel them and do what they need to do, even without autonomy. (I remember concentrating on one Sim at the fishing hole while her mother was writing a book. Forgot that poor Gran needed the toilet a bit more often, but she didn't. When her bladder need went into the red, she quit writing and used the toilet by herself.) I've also had them autonomously try to give their toddler a sippy cup when the toddler was hungry - they still get the 'check toddler' if the kid throws a tantrum or needs food or sleep.
I like the partial autonomy in S3(?) - if you didn't queue something up within five seconds, they'd act on their own. I know there are some things I miss by having autonomy on all the time, such as 'thinking about family' while eating. It would also be nice if my kids, teens and toddlers weren't relentlessly perfect, since I'm not going to direct them to do something they shouldn't do. (Toddlers still refuse to do certain things, especially before they gain thinking skills, but they don't play in the toilet or make messes.)
I would also prefer the option to enable autonomy only for the selected Sim, rather than the other way around. That way, I could see what my Sim wanted to do, and stop them if I disagreed with their choice, but the rest of the family would continue to do whatever they're supposed to be doing.