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Mostly it is the lack of encryption at rest. Evernote already had one suspected security breach a couple years back, so I don’t feel very comfortable putting personal stuff there.

http://www.darkreading.com/attacks-and-breaches/evernote-breach-7-security-lessons/d/d-id/1108909?

Also, Evernote is a bit “big” for just taking notes, which is why I use Notebooks. That’s partially my own doing – I keep so much stuff in Evernote, that finding my way around can be a bit daunting.