Another reason I suspect Skuld, is that there are lots of clues pointing to her, yet Nomura hasn't really ever made her the obvious suspect, as he did very effectively for Lauriam and Brain, and now he has apparently wasted the opportunity. There was a time when Skuld could have come under a lot more suspicion, and that is during Lauriam's investigation with Elrena.
Elrena's Chirithy tells Lauriam that the last time he saw Strelitzia's Chirithy, they ran off to find her when they saw Skuld enter the warehouse. Reasonably, Lauriam immediately goes to talk to Skuld, and this is what we see of their conversation:
Lauriam: Sorry, there's something I have to ask Skuld. Skuld: Huh? Me? (Later...) Lauriam: I see... Skuld: I'm sorry I couldn't be of any help... Lauriam: No, it's fine, thank you.
So we don't know know what precisely Skuld says but it doesn't seem to raise suspicions among the group (the other Union Leaders are present too). What actually happened what that she and Player entered the warehouse, spoke with Gula about the Lost Page (after an encounter with darklings and dark Chirthy), then exited and splitting up from Player (after they do not accept to join the Dandelions).
I assume she doesn't tell them about Gula, the Lost Page, or the Dark Chirithy because otherwise you would really think that one of the other leaders would find it interesting and want to talk more about it.
Then Brain muses on who Strelitzia is looking for ' a really quiet person who doesn't join the Dandelions' and Ephemer suggests Player, which surprises Skuld, though you would think her own recollections would have allowed her to make the connection herself. The scene ends thus:
Lauriam: Do you know who it could be? Ephemera: They're a friend of mine.
This wording makes it seem like maybe Skuld didn't mention that it was Player she was with when she entered the warehouse, though we just don't know.
In the next update, Lauriam does talk to Player and after another hidden conversation (not surprising for Player) it seems Player doesn't know anything about Strelitzia's fate, however we then get this:
Lauriam: But it does clear something up. Ephemera: Yeah. Player: ?
Lauriam then leaves and we don't get much of a clue as to what has been cleared up. I think it's likely to do with his time with Skuld though, either her presence, their conversation with Gula, or her trying to recruit them into the Dandelions, as Player's going into the warehouse with Skuld is the most relevant thing they could talk about.
In the next long scene, after Elrena talks about the glitch, we get the flashback of her Chirithy talking with Strelitzia's, showing Skuld and Player entering the warehouse, then Lauriam goes to consult Brain. Up to now, it really seems like the spotlight is slowly being turned on Skuld, however there's a massive shift at the end of the scene when Brain says that he will 'become the virus', effectively directing all our suspicions to him and away from Skuld.
My point is that I feel like Nomura must have been aware that it would be logical to cast suspicion on Skuld here yet chose not to, just as he recently chose to have Brain say that the Union Leaders weren't meant to meet ahead of time, logically pointing to Skuld, only for him to disregard that a few months later by naming Ven as the replacement.
Either Nomura is writing things this way to be very tricksy and hide clues pointing to Skuld, or he is just lazy and couldn't be bothered to even put Skuld in the frame for a bit, despite his having set her up, and rushed to reveal Ven as the replacement, even though there are far fewer clues for him and it contradicts the rule stated 4 months ago. Also the animators got lazy and forgot to make Skuld look surprised when she heard Strelitzia was meant to be a leader, though they made her look surprised at other moments in the same scene.
I have really enjoyed watching the UX cutscenes and want to say it's well written but I don't think I will be able to do that if Ven really is the replacement and not Skuld (maybe it could work if Skuld is the killer and made Ven the replacement but I think her being the replacement herself works better). Sorry for the rant but I just feel that it would be so much better and more internally consistent for it to be Skuld.