There is a practical limit to how big and heavy and aircraft can get and still be viably carrier based. Not just takeoff and landing, but fitting into the hangar deck. That's what really killed the naval variant F-111.
The Air Force doesn't have a similar concern - if they need to make it bigger to carry a certain weapon system or radar, so be it.
What does make sense is developing common systems and avionics - especially now days where such a huge amount of money goes into the electronics. That's basically what Boeing did with the 757/767 - different aircraft but with a common flightdeck and systems.
Of course, that requires a high level of cooperation between the different services, which is far easier said than done.