I think FO3 would prepare you better because it's an urban environment. Maybe. Chances are most people are NOT going to be wandering around in the desert. They are going to go where there is more shelter and places to hide. Personally I'd hole up in my house with all my guns loaded and ready. There are plenty of shopping centers around to go to for supplies. FONV wouldn't even prepare you for what it's like to REALLY be in a desert environment. You are not going to find bottles of purified or even dirty water just waiting for you in abandoned houses, maybe at first, but it won't last long. And that will be your main concern because it is really really dry in the desert and you'll need to consume mass quantities of water if you plan on walking anywhere. Which you wouldn't because it's harsh. Dry skin, chapped lips, sunburn...not fun. Plus you are going to REALLY want to know how to use a gun, which in reality a video game can't teach you. Videos games may give you somewhat of an idea of what it's like, but the reality is much harsher.
Apparently I need to point out once again that, after the flow of supplies to a city shuts down,
urban equals death. How many farm fields do you have in your city? Super high population density is only possible with the constant input of food from the places that grow it. Once you no longer have fresh food arriving from hundreds of miles away, you have absolutely insane numbers of people that are all starving to death together. It's going to get ugly.
As for water, how long do you think potable water is going to last in an urban environment after there is no power to run the pumps, filters, and treatment plants? Also consider that without power, the sewage system won't be working either. Why hello there Mr. Cholera, how have you been? We haven't seen you in a while.
You could survive after the majority of dying has ended by moving soil up a rooftop. Which would also be highly defensible, since you just have to knock out a few stairways and use ladders to get to your eyrie, which you pull up if attacked. Trap rainwater, maybe even toy with wind power since there's a good breeze up there. But this is only going to be a possibility after a few years have gone by, for the very lucky few who got out of the city after the bombs fell and then came back later for the good scavenging. Right after the event your first order of business is to get as far away from the city as possible with whatver tools you can carry.