If I'm not mistaken the Google Auth app is nice in the way it doesn't store your data on servers, right?
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.