One is the migration path from Evernote. If you look at all the current notetaking apps, none of them seem to have capitalized on the fact that there are lots of unhappy Evernote users out there who would kill for a smooth, painless migration path. Instead, these apps ask you to export your Evernote notes as HTML, something which Evernote only lets you do for a single notebook at a time. I have lots of individual notebooks, so this would take forever. Plus, you lose folders and images this way. Why not just write a small app that scrapes the whole Evernote database? Last I checked, it's an SQLite database!
The other is the lack of offline search. This isn't a dealbreaker, but it seems pretty suspect for an app like this. Losing cell service completely is one thing, but shouldn't it be "offline indexing first" anyway? Obviously it has all my notes synced at all times. I want the search to be lightning fast even if I'm on a slow connection.
It seems like "attachments" (files like PDFs, and also images) are not stored offline, either. In the iOS app, clicking on a file or image brings up an S3 URL inside an embedded web browser.