Unfortunately, http://fermatslibrary.com/ is down at the moment so I can't comment with an informed opinion.

But there are two killer features that most annotation software fail to supply:

1. print-ability. Physical copies are important.

2. Accurate rendering (related to 1). There's a pretty high barrier to overcome before someone else's inline notes are more valuable than knowing that I'm looking at exactly what the authors intended for me to look at.

That said, the scientific PDF annotation space is ripe for disruption. IDK how meaningful that market is (directly or indirectly), but someone could definitely step in and own it with something that's even an iota better than current options.