Why is he wanting a tall storage cubby? And how deep does he want the cubby?

If it is a narrow depth cubby, I'd get rid of the window in the closet and put the cubby there because you are correct in that you will not have enough hanging space. Plus where will you hang things like dresses if you do double rods on both sides?

Closet design is a subspecialty. You need to determine how much you want to hang, long versus short, shoes, chest of drawers, a place to set things down, belt and tie storage, and a bench to sit and put on socks and shoes, There are planners available on website with closeting options. You should cover the window with a blind and utilize that space, too. It can get a little complicated, but if done properly it will work like a smooth oiled machine.

As illustrated on the plan, I see some wasted space.

You can hire a company to design you a plan, make it and install it. Or, you can buy systems from HD, Lowes, IKEA, or the Container Store. You can build it yourself. Do as much planning for this as you do for your kitchen.

A well planned closet is the key to organizational happiness.

DH gets more closet space than you do? I understand that his work gear requires space, but that will leave you with 4-5' of closet space on the long wall. Yes, lose the water closet. Instead of a tower, how about a wall of cubbies on the end wall?

I totally understand the work gear. My dh actually has his work locker downstairs and a whole wall just like that with short and long sleeved uniforms - even with our new build much more organized closet there just isn't enough room! Will the 5' section be double rods?

I too would ditch the water closet and rotate the toilet but that's such a personal preference so....YMMV.

As for cubbies - will you have a space for 3/4 hanging for dresses or anything like that? It would leave enough space for a nice sized shelf that you could fit with plugs for charging. How much stuff does he need shelving for?

Do you have space for linens in the master bath or are you trying to incorporate that also? Our closet is similar to yours but we split it one side is mine and the opposite is his. The uniforms do take up so much space, have you measured the space they currently are requiring?

I will try to post a layout of our closet organizer later, I can't seem to locate the drawing right now.

Okay here is what we have - my side I have plenty of room. His side has just his day to day clothes - no uniforms and it could be a bit bigger. Do you have dressers in the bedroom? We do not - all of our clothing (besides work uniforms) is in this space. Hopefully it helps with perspective.

My side - far right is linen area as the bathroom is off this side.

His side - bottom has 2 drawers now:

overhead view:

FWIW this seems to really make a large impact on usable space. I would also make that closet door a pocket door as it may be left open mostly and it would allow more light into the bath? That's just me since that is what we have and I love it:

Can we see the layout with the master bath and bedroom?

Our layout is also similar--about 5.5' d by 8.5' l rectangle. We don't have a window, and the safe is in the spare bedroom's closet. On the left wall (5.5') we did a long hang rod next to a floor to (almost) ceiling shoe rack. The back wall has double rods on either side of a half wall of cubbies for folded tees and jeans. Under the cubbies is a small dresser. The right wall is all double hang. Any leftover space has shelves for luggage, etc. DH's uniforms take up one of the short rods, but we manage to have another short rod completely empty.

Throwing it out there to help you brainstorm. I found easyclosets.com to be a helpful tool designing what I wanted--then giving that to our builder. Measure everything! Shoe heights/widths. Folded clothes depth/width. Rod length currently using. It'll help.