Huge gap in animation fidelity between the two games.
Simply making minor adaptations to existing rigs and animations may not be enough. I'd gather that a large chunk of the animations are mo-capped as well, which means re-doing mo-cap sessions, fixing those animations, etc. In addition to this, the complexity of the AC animation system is FAR beyond any comparable example. This is accentuated because the AC series is animation-driven to the point where it negatively impacts gameplay (try doing a 180; see how sluggish the responsiveness there is).
We also have no context as to what the competing features are. Ubisoft says there are 8000 animations to replace. For the sake of argument, let's say that 3000 of them ACTUALLY require changes to accommodate for a female frame. Let's also ignore the rigging process, texturing, modeling, VO, and more. That's still a lot of animation work, and the producers on the project have to ask:
Do we get more value out of a female character, or could we spend those animation resources on additional weapons? Better parkour? Bug-fixing? More clothing options?
We don't know any of these, but that's what comes up in any prioritization process. Ubisoft being a data-driven company, I wouldn't be surprised if they did market research into the importance of these features as well.
As someone who works with and speaks to animators, tech artists, engineers, and animation systems on a daily basis (with pedigrees like Blizzard, Vigil, Valve, Crytek, Pixar--these guys are no joke), I find it very insulting that anyone can trivialize the importance of properly done, high-fidelity animations. It's not easy. It's not a small job.
We don't know what the context is at Ubi, and they have no need to share it with us. I'm perfectly satisfied with their explanation.