said by Daemon:iTunes always downloads the full OS and installs it. OTA only downloads the changes since the last update.
The difference is which files are replaced--with the iTunes update, it replaces all of the OS files even if some of them are the same copies that were present prior to the update.
The full update is likely to be more stable, as you could have a modified version of a file that the OTA updaters didn't expect to be modified, causing an incompatibility. The full installer will replace all files, and likely replace the unexpectedly modified file, restoring compatibility.
You also have the fact that if the iDevice is low on free space the iTunes method can still update it while OTAs have been known to fail if the device is low on free space.