I always restore as new with any major interval iOS update. I primarily do this to purge the garbage data from the "Other" directory (some of this junk data won't go away until you restore the device as new).
Once I verify the install, then I restore the apps and data from a backup. Always using iTunes, never OTA.
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I maybe misinformed but I don't think there's any difference between either method, except for maybe a placebo effect.
The OTA update is a delta file that only swaps out the change files. The iTunes iOS update is a full installation that replaces the entire system directory.
As a rule of thumb, I prefer the iTunes update because it just seems to create fewer issues. Recall that the iOS 8.0.1 fiasco only affected the OTA updates, because the installation package specified some incorrect files to keep/replace.
Also, the OTA iOS updates require a huge amount of free storage space on the device. For lower capacity devices operating close to the limit, it's just easier to use iTunes and not worry about how to clear out 5+ GB of storage space for the OS update.