Oh gawd i would love that

played Prototype and loved it

In a Fallout would be so cool.
First off the first part of your post made me hit my head on my desk i was laughing so hard

As for a buildable base, that would be cool. You could make a base like the mutants did maybe bring a captive or two back (nudge nudge wink wink)
And if they MUST have fast travel i;d say you get a beacon that lets you fast travel to your home or something like that. I'd prefer not to ahve fast travel tho. I'd rather have to take the nuclear powered steam train to the closest town and huff it over. Kill a radscorpion or 2 on the way

Barge in th front door and yell "Honey im hooooommmeee!' then throw the rad scorpion at her feet and say and i brought dinner!.

First: Glad that amused you. I hit my head on the desk laughing so hard while I was writing it.
Also, I agree for the most part with fast travel. I never liked it. Not in Oblivion. Not in Fallout 3. I much preferred, at MOST, locations at which you might get a 'travel service' sort of option to FAST TRAVEL you to another location in the game. Sometimes it was a one way trip!
The idea of fast travel confuses me. It takes away from the part of the game that really feels the most fallout-y... WANDERING.
You're supposed to be the Lone Wanderer, aren't you?
The Vault Dweller was a lone wanderer.
The Chosen One was a lone wanderer.
(with allies like Ian and Myron... you usually wind up alone again pretty quick anyways.)
And lastly:
After some careful consideration... I have decided that I agree with the one guy who suggested letting the player create their own faction. Certainly that couldn't be TOO hard. One would think that, after all of this time, they could figure out how to do that. The creation of my own particular faction... (be it a business, a merc crew, a band of specific raiders) ... would be right there on the top of my list of amazingly badass things to be able to do. I don't just want followers. I want employees! I want a means of making a REAL change in the wasteland. And perhaps make a fortune too.
Let me run my own caravan. Let me bottle water. Let me be the Captain of a mercenary group. Let me become a raider king!
I don't just want to JOIN some group and take over.
I want to EARN the loyalty and respect... or perhaps FEAR and respect... of a group of individuals.
And then I want to name them.
And make money off of the effort.