1. When I don't play with autonomy on, my sims will take it upon themselves to try and fill their motives when they're dangerously low. This is a peeve of mine. Are there any mods that fix this?
2. When motives are getting low, sims will look around and start shouting before they do whatever. I remember there was a mod like this for the Sims 2. Are there any mods that disable this?
3. I've never had pets run away until today! I don't have the time to see to them every few hours. Are there any mods that keep their social needs in the okay so that they won't walk around with their heads hanging (and run off)? I tried looking around in MCCC but nothing.

1. I had the same pet peeve until I found the Self configureable autonomy mod: http://modthesims.info/d/602837/sel...mod-scamv5.html
The mod lets allows you to take away autonomy from almost any action in the game. The only problem is that when you blacklist an action, it gets blacklisted for all sims. So for example I blacklisted toilet use and no sim in the game could use the toilet on their own anymore, including party guests and sims on venues. Worked around by placing Talking toilets at every venue and normal ones at residential lots.

3. I don't know of any auto-motive solvers, but try Controlable pets mod: http://sims4studio.com/post/89311
It makes the needs visible and you can micromanage your pets instead of controling them only indirectly.