I have recently format(not just wiping) userdata partition on Note 2 N7100 and Tab 7.7 P6800.
I also restore /data using nandroid and restore internal sdcard by manually copying files. I notice that my devices become much snappier. App installs and opens are much faster. It used to lag a lot when it gets connected to internet, triggering apps to run by Autoruns. After formatting, it just doesn't lag when connected to internet. I noticed that mmcqd0, kworker, system_server now use much less CPU than before formatting. I also do TRIM a lot, and it didn't help the device to become any faster. Both devices were heavily used, stored a lot of files to almost full capacity, cleaned up some space, and stored new files(app and internal sd) again, installed custom ROMs more than 10 times and always install without wiping data/media/, only wiping /data/.
So is it possible that files on those device gets fragmented and slow down everything? I'm just curious why a format with restore of everything fix lags on my device very much.