The reset feature on the phone runs a series of scripts that are suppose to clean the contents of the phone. However, it doesn't actually restore your phone to a pristine OS installation - only flashing can do that.

It's generally better to use flasher because it gives you the most flexibility and allows you to start off with a clean installation. A lot of people have had trouble with SSU (OTA upgrade), either during the upgrade or afterward. Also, a lot of N9s still can't be upgraded via SSU or NSU, but they can with flasher.

It's a little more daunting, since you have to use the command line to do it, but hopefully this HOWTO will guide you through it. If you want to reset everything, make sure to do the "comprehensive" flash that will erase both user data and the operating system/apps.

Edit: Looks like you posted in two different forums - please don't do that, it'll just have to be merged