FONV isn't as extensive as FO 1 and 2 as far as reputation goes, but, when you made enemies, they were always your enemies, which is also true in NV, if you make a group hostile, they are going to remain hostile(for the most part). FO 1 and 2 obviously did it better, as there were global reputations that were not part of faction reputation, so the fact is, it isn't "impossible" to have global reputations, as this was accomplished 20 years ago. It would not be impossible to have this in modern Fallout games. FONV was a start and it COULD have been improved upon, instead of scrapped.
For example, a reputation one could gain for playing an evil character in the older Fallout games was Berserker. Problem was it wasn't used all that much(there are a couple places where this can come into play). Again, all of this could have been improved upon and the end result would have been a lot more fun. IMO, the game should have faction reputations and global reputation, pick say roughly 6 global reps your character can acquire, a low enough number to not complicate design and high enough to offer variation and fun.(FONV didn't have global reps like FO 1 and 2 did, hence why it wasn't as good as the originals but still better than 3 and 4).