So if you are rooted and able to back up the APK + data with Titanium Backup it is doing a fairly good job. It is what I have been doing anyway. Obviously Aegis offers more functionalities, so if this app is going to stick around, there is a pretty high chance I am going to switch over.
Yep! Hence The Google auth app was widely recommended before when there's not that much good alternatives. As with a rooted phone + Titanium backup, that's what I did in the past too. It's nice to have in-app password encryption though; just a small extra layer of security.
If you're going to switch over and you have a rooted phone, switching over is going to be A LOT easier. Aegis has an "import from app" feature if you have a rooted phone. It can grab the backup codes off Google auth. I suggest trying it out.