I could not agree with this sentiment more!
Endnote currently allows ONE libary to be synced online which means you have to store multiple projects in one giant file and create groups for each product.
I have over 200 projects and typically create a Library for each project and merge what I need if I need to.
EN8 has obliterated the functionality of working through SugarSync, my chose sync program, which worked flawlessly before hand.
The current EN system is short sighted and, to be quite honest, one that strong arms users into a proprietary system that is not functional unless you are willing to create one master library and work out of that. Let the user choose please.