Honestly I feel like Xion must have been planned or at least under strong consideration from early on, even if her inclusion wasn't always guaranteed. The main reason I think this is that the "Real" Organisation 13, seems to largely consist out of Final or Major bosses from previous entries.
Ansem (KH1, Riku: CoM), Marluxia (Sora: CoM), Xemnas (KH1, Sora: DDD), Xigbar/Braig (Aqua: BBS), Master Xehanort (Terra: BBS), Terranort (Terra & Final Ep: BBS), Vanitas (Aqua & Ven: BBS), Young Xehanort (DDD) and Dark Riku as an enemy Riku stand in (KH1, Coded, Days).
Xion not being included would have made her the odd one out. I mean technically with Re:Coded, there'd have also been an argument for there to be a Roxas in the line up, which kinda tracks with him being the original 13th candidate.
Saix, Larxene and Luxord are kind of outliers, though all of them are part of the final Boss "rush" of previous games. Okay with Larxene it's a bit of a stretch...