You're comparing skateboards with airplanes. Readdle's alternative to GoodReader is PDF Expert, not Documents. Documents gives zero annotation options, so it's no alternative to GoodReader for me. PDF Expert can't quite compete with GoodReader, either; especially the iPhone version is inferior.
By the way, both are Russian apps.
I would blame iOS 7 for any current GoodReader issues. (Not observed by me so far.) iOS 7 is an unmitigated disaster in every respect, creating lots of problems of all kinds on both iPad and iPhone for me.
If I could return to iOS 6, I'd do it in a heartbeat.