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First impressions are...
The desktop app is a little flakey. Early on, I had a crash that corrupted my database. So, I now backup my database after every session of adding new papers or organizing. Multi-selecting too many pdfs to add will cause the app to crash (and possibly corrupt your database). I only add 10-12 at a time.
Nested collections would be nice. But I'm still trying to figure out the right combination of collections and tags that is the most useful.
A few more document types would be nice, like a presentation type (pdfs of slides, etc)
Until they get a subscription model going, the 500 mb of space on the server seems too small, so I don't really have any papers stored on the server (so I can get at them from anywhere).
Haven't used any of the collaboration features as I haven't found anyone I know with similar interests who has signed up. Hopefully, sometime soon.