I'm a bit confused. Do you now have 3 toilets in your home? How many bedrooms? It would be most helpful if you could sketch a simple layout of your house so we could see what size space you are dealing with.

I see absolutely no reason to have two toilets in the same bathroom.

So you’re going from 3 bathrooms to two, and one of the two is solely used for the primary bedroom which means every other bedroom and/or guest has use of just one bathroom. I’m all for using your house to suit you and not the imaginary people that may buy it 20 years from now, but removing a bathroom can be a big downgrade depending on the house. And two toilets in one bathroom will always sound weird unless it’s a dormitory

Yes, I agree with the opinions so far about 2 toilets in the same room being weird, and also that it might not be the best idea to remove an existing toilet. I'll try to get a basic sketch uploaded so people can see the current layout. I'm very hesitant to remove an existing toilet as well, and yes to the question of how many toilets are in the house - there are currently 3. Of course there is more to this story, probably like in most remodeling projects. The small, guest bathroom in question used to have a small shower in it. Whoever added the master bedroom area, abandoned the small guest shower and turned it into a closet (but left the tile floor - so that's why I know what it used to be). Then, I highly suspect that when they added a big, jetted tub to the master bath - they used the drain from the abandoned, little shower, but ran the drain pipe over the top of the concrete slab floor into the old shower drain - hence I think that the drain actually kind of runs uphill for a bit before emptying into the old shower drain, which might explain why the jetted tub/shower doesn't drain very well and we have to use a plunger while showering to get the water to go down the drain. I can kind of see this part of the plumbing from an opening in the wall under the master bathroom sink vanity, but won't know for sure until everything is removed. Part of our thinking in abandoning the small guest bath is so we could remove the big soaking tub and use the old shower drain to once again be the shower for the master bath. I know this is hard to imagine without a drawing, and I'll try to get one uploaded. There are a lot of quirks to the current layout, including that someone in the neighborhood said that the current master bedroom was once a family room with a pool table in it, which explains why nothing seems to go together and everything is an afterthought. Many thanks to those who have given their opinions!

The grid squares represent 1 sq foot. This is a quick, rough diagram of the rooms involved.