For me the biggest thing is having a full backup. I don't want app developers to be able to decide if data on my phone gets backed up or not, that is not their decision to make, it's my phone, goddammit. And I want to back it up to where I want to. Also in a similar vein, having access to all data on my system. In the worst case scenario to troubleshoot things.
Also, there are so many useful tweaks where I just wonder, why the fuck is this not part of Android, or why do I need root to change this? Like being able to rotate my phone 180°. Or having a battery bar instead of a battery icon. Or showing more icons in the notification area. Or not having it close apps after I haven't used them for a certain amount of time (I left that video open for a fucking reason, maybe because I wanted to finish watching it tomorrow or the day after).
Oh, and an ad blocker that is much better integrated into the system is pretty nice.