That's what I thought. If they were last minute decisions, then why do you spend nearly half of the story mode playing as Alpha Patroklos? Pyrrha Omega was probably intended too.
A ultimate version of Pat and Pyrrha imo was intended super early in development for the reasons of storymode (brother and sister taking properties of soul calibr/edge). What is baffling on the surface to the rest of fanbase is why would the soul calibur moveset have to settle on something related to a japanese geisha who was a probably the character least related to the soul calibur/edge story. At least Talim had her supernatural wind powers to feel soul edge, while Setsuka is basically a side-quest for Mitsurugi.
The answer may be a combination of the fact that Daishi really loved the moveset and couldn't bear to part with it, as well as having a JF heavy moveset justified for being intentionally top-tier and being worthy of being the representation of soul calibur's power both story and gameplay wise. You can see it as 2 birds with 1 stone solution. I personally don't like it but I can understand.
A similar solution could have occured with with Shin Pyrrha, as they always intended her to be super strong either, but having her take the moveset of iconic JF heavy moveset of cerventes would be too much (since that would mean eliminating cerventes from the roster) and no one is replacing nightmare (as evidenced in soul calibur II) and so unfortunately she ended up being too similar to regular pyrrha.
I'm kinda glad that they didnt end up making alpha-pat and omega pyrrha mimic characters. While it may seem like a convenient solution for Soul Calibur 5, (having them mimic movesets, but with unique CEs) the future of the Soul Calibur storyline rests on their shoulders so if they return in SC6 as mimic characters that would be completely unacceptable. I can't recall any fighting games where the main protagonist is a mimic character (call me out if i'm wrong).
If I had a choice, Alpha Pat and Omega Pyrrha would just be skin swaps of the normal versions. Maybe i'm thinking Zas-->Abyss as an example, but at the same time Abyss had eligibility issues as well. I don't like the taste of having setsuka's moveset being intentionally stronger, despite being stapled on to Alpha Pat for flavour reasons. Can anyone comment on the differences between siegfried and nightmare in SC 1 ?