We went again last year with the kids and I love the historic dockyard, although I still haven't been to the Royal marines museum, and I haven't been to the submarine for 40 years (am now sl. claustrophobic, so not my thing anymore).
Those two bits aside, which are far from the rest, the rest of the museum is very compact and easy to navigate in a day. Don't feel obliged to tick every box, some parts are just not interesting unless one is a serious enthusiast.
If the weather is nice, I would note the timings of the harbour tour after entry, and aim to line up 10-15 minutes in advance, since it can get full. Alternatively, if parked at Gunwharf, one can do that last, and get dropped off there, saving a 10 minute walk at the end of your visit.
Although it sounds gimmicky, the newish "4D" experience at the Mary Rose is actually both fun and moving, we did it twice!
tb