Fairly good points.
The UI is pretty good so far (in terms of the community edition at least). There are definitely bits I find a bit counter productive at times, but you can work around them.
Notifications: A great thing to have, with a bit of a stickler to them. If you mean 'email notifications', then you end up having to add an external process that checks for out going notifications to send. In the hosted version, this is easy. If you have your own server, this is easy. If you are like me, and run it on a hosted web server, then this is not easy at all.
Wiki editing of notes, and the currently implemented WYSIWYG editor are at odds with each other. You would have to choose one over the other. Or you burn valuable development time creating a whole new technology to support both modes in real time in parallel. That time is better invested in bug bashing and feature polishing.
Folders: A great idea that can be used in several places to organize information. Files, Notes, etc
Native apps: Kind of inconsistent for a web app, especially this early in its life cycle. To implement it you have to keep large copies of all the data on the mobile device and try and sync it to the master system when you still have connectivity. It is better to focus on compatibility with more browsers, or better support in currently used browsers. Pretty much anything based on Webkit has problems with Description / Comment boxes (at least in community 2.2.1)
Cloud sync? This is the cloud. What more do you want to sync it with?
It would be sweet if it could make your documents available as a webdav site (like dropbox / box.com)