Because the Brotherhood is about the preservation of technology. I'm pretty sure that the APA MK II is a much more advanced model of power armor than the T-51b.
I don't know man, I have no idea what's going on with the APA models anymore. Both the MK I and MK II were better than the T-51b in Fallout 2, but in Fallout 3 the MK I wasn't present while the MK II is barely any better than the T-45d and the T-51b was the best armor in the game. Generally a weapon or armor's in-game should statistics reflect how its portrayed in the story.
Assuming that Advanced Power Armor is superior to the T-51b as it's supposed to be though; It would be in the Brotherhood's nature to use the most advanced technology available to them. We can only assume that they didn't find enough suits of Advanced Power Armor and opted just to study what they did find. They presumably still don't have the capability to manufacture such advanced technology after all.