Comparing internal and external SATA

It depends on the purpouse of the drive.
For a backup device, eSATA.
Boot or storage drive, internal SATA.
You will have the same performance from both interfaces so it really depends on what your intentions are...
 
Use internal for information you need to be online all the time.

Use external for data you need to be able to take away from the computer, such as backups or transporting data to a friend's house.