Apart from being automatically updated, and even if you apply updates manually, you only know about possible disadvantages once the update was done. So my recommendation goes in a different direction, namely: being able to restore the state before the update was applied, so you can "roll back".
For this, I recommend using AppMonster (or rather AppMonster Pro, as the Pro version can do all required stuff automatically in background, so you cannot forget it). This app automatically creates a backup of each app's
.apk file whenever the app is installed or updated. It also takes care about only keeping a configured number of backups, so you don't risk running out of space. If you don't like an update, you then can simply launche AppMonster to restore a previous version.
I'm using AppMonster for years already, and can heartily recommend it. And as to your original question: I have auto-updates turned off, so I can manually decide which updates I want and which not. For some apps, I prefer the version I'm currently using for reasons like removed functionality, less overhead, and more.