Updating iOS using OTA vs updating through Itunes

well, if you plan to jailbreak, it is best to update through iTunes, but if you just plan to use your device, I would just go with over the air updates.

Given that Apple allows people to update iOS either way, they are both good choices.

However, my long career in IT leads me to be wary of overlaying new stuff on old, and I prefer to do the iTunes method. While I can't say as I know this, I assume the larger file is there to do a complete replacement, rather than a patch.

Well the big notice difference as you mention above is
Starting with
OTA/ Over the Air
For some people who are confuse OTA and Over the Air means the same thing.
FILE size
The OTA updates provides a delta update only while iTunes provided the whole build.
Delta include small size while whole build unpack the big file using PC or Mac
on my experience I have 2 iPhone's
updating via iTunes the file size to each device is completely different
iPhone 5 1.5Gb
iPhone 5S 1.7Gb
and I would understand that for newer iOS devices is to much larger

ADVICE from apple Tech support
If there is a problem after installing the delta update OTA, restoring the iPhone with iTunes to install the whole build for the update may resolve the problem.
The most common problems are: Battery life, Wi/Fi Problem, BlueTooth Issue, or Software Bug.

PERFORMENCE
Using iTunes The full update is likely to be more stable
There the possibility of minus glitches

EXPLICATION
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.

ACCESSIBILITY
Using iTunes you are able to know the situation in which the update process
extracting, installing, verifying software with apple, iPhone rebooting and all those details that updating over the Air or OTA couldn't announce
While keeps silence through this process only show the apple logo on the screen and some progress indicater but impossible to read for voiceOver it takes about 10 minutes or less.

I actually do both. I hit the download only option then save the ipsw somewhere else. What the phone does is download what we call the delta update, that is, it only downloaded files it needs.

The delta update takes longer, about 10-15 minutes whereas the update with iTunes once you download then later choose it, let's say if you need to restore your phone, takes only about 5.

Take care.

I've never had a single issue with using over-the-air updates. The only way I would ever choose iTunes is if my experience with using over-the-air updates had had an issue but honestly, I haven't had a single one and I've been using iOS since 2012. I guess the only way to really know the difference is to try both and see which way you prefer. There is no right or wrong way to do it, but people do have their preferences, and when something works for someone, they're going to continue to use it. I personally hate the thought of using iTunes for anything other than buying music and the very occasional app, I think the software is clunky and...well, the design on the windows side of things isn't exactly stellar. You mac folks have it a bit better from what I'm told, so I understand why you'd use it. Either way, that's my answer, for whatever its worth.