Its not a plot hole, this story is actualy very well rounded if you ignore x-2.
It's simple, chibi seymour completes his pilgrimage, and then does not battle sin. And so anima's fayth is moved too baaj ( upon seymours request i beleive).
Anyone can call on this aeon if the aeon is willing, only difference is - anima is more powerful in seymours control due too the strength of their bond. It's the (cheesy i know) bonds power gives the aeon the strength too defeat sin.
Once yu-yevon posses the aeon, that bond is cut and from what the game explains, severing that special bond will kill you.




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