Hypothetically, they could have planned on both Isabelle and Isaac and were forced to cut the Isaac portion, but nah, I do agree that Isabelle was for sure planned.
Concerning the new Card Theory, while I don't subscribe to it, it is a little bit suspect that the two empty boxes appear again. It seems to be more than a coincidence, however, I think that the reason is because, from a graphic design standpoint, it works numerically. It is funny though that one of the blank spots is next to Ryu, but it's on the wrong side of him for it to be Ken, which is only further proof to me that the Box is a work-in-progress just like how this seems to be a snapshot of the currently revealed characters.
So, yay, hope! It may be a point for the Box Theory with the matching numbers, but it doesn't all add up and still can be a bastion of hope for everyone else!