A thing I noticed last night.

We had a 4 player game going in the Capital Wasteland, and 3 players ended up with one faction (BoS) and I was Enclave

They all worked on BoS, and got to each locale faster than I could even with me making beelines directly to each one.
First, should there be so many +X faction cards, and second, should having more than 1 stack? Two players hit 8 influence thanks to each having 2 BoS faction cards. I found nothing in the rules that state you cannot have more than one (though logically, it seems silly that they would stack like that).

Yes, there are far more Faction specific Agenda cards than non-Faction specific ones. So it's very likely that you'll end up with at least two of them each game. Some people have made house rules that each Agenda card of the same type only adds +1 Influence but that may make it impossible for some players to win the game.

The solution, unfortunately, is for FFG to print more non-faction Agenda cards so we can adjust the numbers to taste. Might or might not happen.

Personally, I just ignore the victory threshold and play until one faction rules the wastes and the player with the most Influence points wins. Even if it's less than the required amount.

Each Agenda is considered one Influence but you can only have 4 so in theory you could trash other faction cards you have to try and get better agendas. In the one experience that I have played so far agendas and influence seem to be the Heel of this game.