[AT&T HTC One (M8)] redpoint73:
SuperUser is same as root, and is fine.

When I say "modifed by root" that often is when a user deletes "bloatware" they don't want, or adds apps, or modifies apps in the system partition.

If you didn't explicitly do any of those things, you should be fine. You will know this is the problem when you install the OTA, as the install will fail with the error message that the "system has been modified".

RUU = ROM update utility

RUU is super easy, you don't really need much guidance to use it. LOCKED or RELOCKED bootloader is required to run it (UNLOCKED if okay if you have s-off). PC required, and the RUU

will

wipe the phone (so backup any personal data you want to keep, into your PC, cloud, etc.). Aside from those points, RUU is a self-explanatory executable (.exe) program that runs from your PC, and simple to use.

Relocking the bootloader is accomplished easily with a single fastboot command (after connecting phone to PC and booting into fastboot mode): fastboot oem lock

This is also assuming you did the bootloader unlock yourself, and therefore have fastboot/adb setup on your computer.

Running the RUU itself (after relocking the bootloader) is very easy. Boot into OS (some folks have better success being booted into fastboot mode, but I think the RUU is designed to run when booted into OS), connect to PC, then just run the RUU executable on your PC. The RUU executable will then just guide you what you need to do. Its mostly automated, you just need to confirm a few dialogue screens, etc. The RUU will reboot the phone a couple times, install the needed files automatically, and that's really it.

However

, since you seem confidant you already have a stock ROM and corresponding stock recovery, I suppose the RUU doesn't gain you too much. But if you hadn't done those steps already, it often saves folks the hassle of tracking down the right stock ROM and recovery for their CID and current firmware. RUU in my opinion is a cleaner install, as it installs a complete stock image (not just updating piecemeal, like an OTA often does).

Also, since OTAs typically need to be installed in sequence, you will probably need to OTA to 2.23 software, than another OTA to 3.42 software. As RUU is a complete image, it would get you to 3.42 software in one fell swoop.

One other thing to note, is that if you are for some reason

not

connected to AT&T's network (using another carrier, another country, etc.) you will not get any OTAs on the AT&T branded device. AT&T oddity here, most other version will still OTA, even when not connected to a specific carrier. In contrast the AT&T RUU is able to be downloaded and run by anyone with an internet connection and PC (regardless of country, carrier, etc.). I'm under the assumption that most folks on this forum section are on AT&T's network, although I know that some are not (you haven't stated either way).

RUU links are included on my Index thread under heading "RUUs": http://xdaforums.com/showthread.php?t=2751432

Aside from wiping the phone (OTA keeps user data, but you may end up wiping anyway if you run into bugs after OTA), the other downside to RUU is that you need to relock the bootloader. Then you need to unlock the bootloader again (via the HTCDev.com site, or alternately sunshine) if you want to install custom recovery, install custom ROMs, root, etc.

So the choice is really yours (RUU versus OTA). I'm just giving it as an alternative.