Some observations:

You can't get to the toilet in the powder room without sitting on the sink to close the door. Pocket or barn door would be a better choice here.

Pretty sure (take a ruler to your plans to verify) if the guest room door is open and the guest bathroom door is open, you can see the toilet from the foyer... For sure, from the guest room door.

I cannot tell where the doors are--
*from mudroom to living space? through bev center?
*from kitchen to dining? (no idea)

How will bedroom 6 be used? I notice that it has a tiny closet and shares a bath compared to all other bedrooms in the house... Is it a spare room? Is there any particular reason to make that shared bath be a J&J instead of just a hall bath? I would not be difficult to move Bd 5's door so that the hall extends to the bath, and then both bedrooms would have access to the bath through a single common bathroom door (hence, eliminating the real problem of someone locking someone else out of the bathroom unintentionally... Unless, that bathroom will never really be occupied by more than 1 person because bedroom 6 will be...an office, say. But, I think I'd still think about making it be a common entrance hall bath, simply by moving the door to bedroom 5.

I remember that you had a reason to separate your bedrooms, but I can't remember what. I think it would live weird, to me, to have the upstairs areas not connected. But, if I recall, you wanted that for a particular reason.

Will bedroom 3 have enough light? The only window appears to be kind of small. I guess if it were my house, I might try to get Bed 3 up to the front of the house for better windows and so the closet wouldn't have to have a window.

Those are my additional observations. Good job with the Master WC door swing. :)

If bedroom #5 and #6 will both be used as bedroom and both need access to the stacked washer and dryer, then it would be better to make the bath a hall access with the washer and dryer on the landing and put the door to that bedroom closer to the room.

Thank you, Kirk! Wow, we totally didn't catch the powder room dilemma. We will also be checking on the guest room visible toilet situation. Great observations!

* Yes, the entrance from the mudroom into the living space is through the beverage center. We realize this is probably not optimal for traffic patterns, but we could not come up with a better alternative that accommodated all of our wish list for the beverage center.
*The area labeled "dining area" is actually an outdoor dining area under a pergola. The actual dining room is off of the family room, open to one another.
* Yes, we want bedrooms 5 and 6 separate from the rest of the home for a reason. We will be using bedroom 5 for a home school room. Our uses for bedroom 6 will change over time from nanny quarters to live-in relatives. We'll think about moving that door . . . I can see pros and cons of both configurations.
*And on to bedroom 3. We will be building built-in bunks and this is what we came up with to have the arrangement we were after, and to have the open foyer for the light above. I too admit that it is a travesty to lose all of that light in the bedroom itself. We really poured over this one but this is what we ultimately came up with to accomplish all of our objectives.
Thanks again for your insights!

Thanks, Scrapbook, I like that suggestion!