If you do the official Metro upgrade, you will have to root again. (Its a different method for 2.2) The custom ROMs are already rooted by default. Apps will have to be put back on your phone either using TiBu or through the market. (the market will remember you so you won't have to pay for apps again) Its basically like getting a new phone, where you have to sign in with your google account, etc.
Differences from 2.1:
2.2 is faster, more efficient, adds apps2sd, compatible with apps that require 2.2 or higher, adds flash support, HOWEVER THE ASCEND WILL NOT PLAY FLASH VIDEO DUE TO HARDWARE LIMITATIONS. sorry for the caps, some people can't get that part through their heads lol.
ICARUS is based on the stock 2.1 ROM, tweaked and streamlined to be faster and adds a custom A2sd that moves ALL the apps to the sd card, even ones that are not supposed to be able to, along with the Dalvik cache, which frees up a ton of space.
CyanogenMod 6/7 are built from the ground up using the Android source code. CM6 is built from 2.2 source, CM7 is built from 2.3 source. These are highly tweaked and customized versions with overclock abilities to make the phone run faster. All Ascends are not created equal, so some seem to prefer one over the other.
I hope this clears some things up for you. If I've gotten anything wrong, anybody feel free to correct me.
@Kolio: I did mention Link 2 SD for stock/rooted in my post. Reading is your friend. Lol