In the Nimrod, crew members who sat facing sideways (Acoustics) were prone to motion sickness; they had no windows, and their inner ear gyros were 90 degrees from the direction of travel. So, I would vote facing forward for everyone. Crew intercom, should be as versatile as possible. In the R1, each back end operator could select individually any other operator and join in as many operators as required. That would be ideal in a MPA. Toilet should not be collocated with the galley; anywhere else is good. I could load my curry in the oven while sat down reducing gross weight (which was frowned on) in the R1. Domed windows should still be included, and should be openable when depressurized; a failure of the EO/IR sensor means a return of the good old days of looking out at 200 ft and taking pics. A crew baggage storage area should be considered as a primary user requirement and the floor loading designed to support at least 50 lbs of kit per crew member. R1 crews were limited to 20lbs (12lbs was the actual limit but exceeded on risk) and required the support of a Herc to transport their stuff when detached. Using pressurized launchers allow for high level releases without depressurizing, which required a change to the flight profile and has a very minor effect on fatigue life (frequent de/re-pressurizations hoop stress cycles; albeit to low diff pxs). The rotary launchers on the MR2s allowed sort of rapid releases, but required the aircraft to be depressurized. There were only two single buoy pressurized launchers. I assume the accuracy of sonobuoy dropping these days allows for higher alts (assuming the sea below can be confirmed clear) so dropping low may not be required anymore? Mission planning areas are not required on board; we can talk on your versatile intercom.
It is refreshing to hear that your user requirements are including the crew and not just the mission. Don't forget the ground crews need good access and a means to test/change faulty components quickly. An LRU storage for in flight maintenance is also required; think CoG, access, lighting, and floor loads.
Finally, provide an APU/GTU that can do everything, and if they ever bring flight engineers back, a beer keg dispenser and fat female pax seat in close proximity to them. Good luck.