After reading your post I only see that the AP is working as intended. I assume this was a pretty small map since you only had 4 AI as rivals. Small maps makes for a completly different game. Winning on a small map compared to a huge one is two different things.
As I understand it there were only 2 AI left since you had conquered two which I now assume you had the lead and were now the most powerfull civ and basically already had the game won, you just had to decide how you wanted to end it and the AP saved you all the work of either conquring what was left or pressing eot untill your spaceship was done.
A diplomatic win in the 1200s seems about right what the AP tries to accomplish namely early wins in the game without the need for wars.
I agree that the AP is mostly fine as is. I had previous posted that it was almost impossible to win via the AP early, and that anyone complaining about it just didn't understand it or didn't make important modifications in how they played.
In the game I won, Darius had twice or more land than I did, and had a tech lead. I could have won through targeted beelining and a massive military emphasis (this is marathon, which is certainly easier regarding military affairs), but victory was not at all assured. I also focused on the AP, and if I hadn't, I probably would have gotten a bit more land. So when I won, I had one vassal (who had founded the religion I used with the AP), and there was one weak (mansa) and one super-strong (darius) ai. This was on a small pangaea, which I chose as the easiest possible map to win an AP victory on. I thought that even with that map setting it would be very hard, but it wasn't.
I think the AP is mostly fine as is, but it does need a small tweak, because only a single city is too easy a threshold on smaller maps. To make it more map-size independent, perhaps something like some percentage of the entire world population divided by the number of civs must follow the religion in each civ: If it's 10%, and there's a total of 500 pop points between 5 civs, then each civ must have .1*(500/5)=10 pop points in cities with the AP religion. The numbers are obviously just for the sake of argument, but I think that might help solve the problem by forcing a non-trivial number of cities to have the religion per civ.
However, I also haven't yet had a game where the AP has negatively affected by gaming experience, so I really wouldn't care if they don't change it. If I were to lose a game due to the AP, I'd probably just reload the last autosave, delete the AP from whomever has it, and give myself an engineer with which to rush-build it. Sure, that's cheating, but I play to enjoy myself, not to follow rules that I don't feel enhance my enjoyment or to compare myself with others.