Syncing multiple libraries is a great idea!
I just posted a request to share group sets with endnote desktop with the same idea in mind. I want to create group sets for specific projects to share with my colleagues.
Either one would work. Both would give the freedom to chose how to work. Syncing multiple libraries would open up the possibility for shared project libraries with multiple group sets.
The endnote web option is just not an alternative since it is missing group sets and the possibility to share attachments which are both dealbrakers for me.