The advantage of using NDEF formatted data is that this is more portable across different systems. NDEF compliant data should work not only on Android, but also on Windows8 or Blackberry devices (with NFC).
The Mifare Classic chip is not part of the NFC specs and therefore works only on phones with the NXP protocol software, but on those phones you can easily store data in NDEF format into a Mifare Classic chip.
The destinction to make is more whether a particular device supports the Mifare Classic chip, than whether you want to use NDEF or not.