Have you ever read the Secret Ansem reports? Here's a link, read them:
Secret Ansem Reports*-*Kingdom Hearts Insider
It definitely isn't Ansem the Wise. Not only does he not have a method of getting to the LoD (he doesn't discover corridors of darkness until after he is imprisoned in the Realm of Nothingness nine years after BbS), but he also is the ruler Radiant Garden, not an Org member. He didn't lead the research team, he commanded it. The first six Org memebers were his apprentices, not his colleagues. And the Org was not even formed until after the apprentices became Nobodies (which was nine years after BbS). And it was formed
by Xemnas as a Nobody. And that was after AtW was banished, so AtW never even knew of the Organization until after he escaped from the Realm of Nothingness a year later (as Secret Ansem Report 7 shows).
So AtW was definitely never in the Organization. And his guilt and lust for vengeance came from the fact that Xehanort, his foremeost apprentice, created the first emblem heartless right under his nose, and basically everything could have been prevented if AtW had been a little more observant.
And just for the record, the secret bosses have never been in the next game. It's always in the next
main game (KH3 in this case). Xemnas appeared in KH1 FM, but did not appear in the next game, CoM. He was in KH2. LS appeared in KH2 FM+, but did not appear in the next two games, coded and Days. He appeared in BbS. And BbS is a main game, even Nomura called it KH0. 3DS is not a main game, so I doubt the secret boss will be explained there.