Since the PVP in the game is in a special zone, no matter what server you are on, you can do it when you want, and avoid it when you don't. Villains has their own story arc, and you should be able to play through just fine. If the Villain pop is lower the only problem would be finding enough people for groups, but my hunch is it's not that much lower.
Also, I'd recommend experimenting with toons in all three settings, just to see what you like best, or as something to change to on a day you feel like not being a villain.
Don't worry about noobishness, the game is scaled anyway, and there is no permadeath, just pride hurt if you happen to get owned.
(take all this with a fairly large grain of salt, because I'm just getting back into the game after a six year hiatus. Some of my recollections may be less than accurate, as I haven't even gotten to the level of PVP possibility yet this time around. Spending too much time enjoying teams and re-learning how to use the powersets.
Glad to have you aboard! Hope you have a great time. Don't be afraid to ask peeps for tips in-game either, COH players tended to be a pretty helpful group back in the day.