I agree that it would take too much work, and we always have mods to change things like this, but in the next Fallout game I would like to be able to continue after the end, or not have any special items in the ending, like the Legate's armor.
I would like a more interesting main storyline, as the was almost no choice on what you could do in either Fallout 3 or New Vegas.
Now before you say the New Vegas storyline had lots of diversity, hear me out.
NCR - Find which factions to side with/remove, win second battle of hoover dam...