I like the fact that you can easily create to do lists in Evernote. What I miss however is the ability to filter out completed to-do items (checkbox marked completed) within a note when using the advanced search capability. As the list of completed to do items becomes longer, the incomplete items become more difficult to spot.
A simple alternative would be the ability to sort items within a note based on the to-do checkbox status. That would allow you to display the incomplete items at the top of the note.