Oimelwutz, my husband’s aunt has MS and has had it for quite a long time. For her, it progresses very mildly, but by now (she is approaching 80) unfortunately the wheelchair is a fixed part of her life. From experience, I would definitely advocate for an open living area with a kitchen, especially under such circumstances. You don’t change rooms so quickly when walking is difficult.
By the way, it takes a very long time with MS until you can no longer stand; standing usually still works even when walking is already difficult.
That means for the kitchen and bathroom: you probably do not need to include sinks or work surfaces designed for a wheelchair user in your planning yet. Rather, something like a chair where your wife can relieve herself if she works in the kitchen for a longer time.
A guest room upstairs is a great idea at first thought. However, our aunt, as she became increasingly immobile, got a physiotherapist who visited her at home. That was a huge relief for everyone. Additionally, she has had a home trainer and a few other devices for years that she uses very consistently. That is something you should consider. Such a small "therapy room" is really priceless! And you could, for example, use a guest room that is only used sporadically for that. Consistent exercise and training are an important part of therapy for MS. I would not overlook that and just dismiss it with a "there are no therapies planned at home."
You have now drawn in your current furniture and your couch is not very large. I would also plan a bit more space for the future. If your wife becomes increasingly restricted, that may also have an impact on a sofa she can use well, or a suitable seating furniture will then be purchased to support her. So I would leave enough space for such eventualities.
And one tip off the house planning topic: please google Sven Böttcher. A writer/screenwriter who himself is severely affected by MS and has gone his very own way. Some things he says I find outrageous, but many are very thought-provoking, and considering that he had a very severe progression, was almost immobile in a wheelchair and considered untreatable, and now lives almost pain-free at home, has not used a wheelchair for years but rides a bike instead, I would like to recommend you possibly get inspiration from him.
He attributes the outbreak of MS in his case to living in a house that was treated with some wood preservative that is now considered highly problematic. His consequence was to sell the house and build a new one for himself and his family, very strictly according to ecological aspects. Reading him, you can easily understand that. Maybe a point for you to think about when you are building now.