I really like the "B" plan. Just one question, why are you putting the master toilet in it's own room back in the corner? That is taking up space that I think would be better used as closet space. If you push the toilet forward and have it at the end of the vanity the smaller of the two master closets could go back all the way to the corner making it much bigger. Moving the toilet like that makes the layout of the bathroom almost exactly the layout of my current master bath. We have a 4' high pony wall at the end of the vanity that gives a little separation and privacy to the toilet area without walling it off.

I'm with Enduring in that I would prefer the space given to the closet instead of the toilet. In the last house, the toilet in the master was crammed into a tiny space shared with a tub/shower combo. Really, really disliked the space. Would traipse down the hall and use the other toilet. (I used the shower in the master only one time in all of the seven years that we lived in that house.)

Also, I would not put a tub in but that may be just me. (The house already has one tub.) I would much rather clean a shower once every six weeks or so (we squeegee after a shower) than have to clean the tub (bent over and on your knees) every single time it is used. Tubs use a lot of water vs the lo-flo shower heads. But, if you love tub baths and routinely use a tub to bathe, that's another story and you'll want to include it in the remodel. (If you're thinking a cast iron tub, the floor framing will probably need to be beefed up.) Not a huge deal since the ceiling below will likely be torn out anyway for the plbg. changes.

The other thing I see as a problem is the door opening directly in front of the vanity. That is going to be a pain if this is a shared bath and someone else is standing in front of the vanity.

Plan B looks great. I love a toilet in its own space. what did you end up doing?