I think you will need to provide a layout including measurements to have any kind of meaningful input. That said, I would get rid of the tub because that is a terrible shower. My preference would be to have a great shower versus a tub and a cramped shower. When I remodeled I got rid of my tub/shower and replaced it with a beautiful functional walk in shower. If you must have a tub at least consider a tub/shower because it is far more comfortable to use than a small stall shower like you have. I prefered using my tub/shower combination to the stall shower in my guest bath which I used for a few weeks after an operation limited mobility. I doubt whether you have enough space to have a comfortable enclosure for the toilet but you might be able to move in to where the shower is. Depending on your budget and what lies below the floor it is theoretically possible. Whatever you do get a skirted toilet so those unattractive traps aren't showing on the side. Skirted toilets are sleeker looking and easier to get clean.

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IMO you do not have space for anything except the tub and shower and I sure hope you have tested getting in and out of the tub they are a PITA to get in and out of . look best in designated space with no other thing next to them you already have an issue with the window placement from what I see . IMO a much better choice would be a really nice deep soaker tub and shower on that wall and of course that window will be an issue with whatever you decide unless you do the soaker there and the shower somehwere else if did that then if you insist on a FS tub that would work in that space. BTW I have never seen a hotel with cubbies between a tub and shower .

Well it depends on the size of the transom. A traditional transom will not. if it is a larger and or operable transom possibly. A lot depends on your ceiling height as well as the outside elevation with that. If light is your goal you can do both if it works on the outside elevation. Also you can do a regular size window inside a shower. Or two smaller square windows.......the possibilities are endless but I try to not elimate existing windows where possible especially when it gives the opportunity for function and light. lower cabinets although tall ones.....i would go counter height with window above.