Back to the original question, the services have input, but the political realities are often very complex, and often driving, factors. The US services do not seem to be the ones driving combined programs, it has usually come from higher in the organization, namely the Secretary of Defense and senior Pentagon managers, Congress and other pressures for jointness and perceived cost savings. If it were left to the services they would prefer aircraft that best suit their unique requirements. Cost realities do come into play, and the services sometimes realize that they need to bundle programs, and it would be cost prohibitive to have multiple programs going at once- and the fact that if a program gets to "too big to cancel" that might be better to have a "good enough" aircraft than no program at all. The services do provide requirements (often changing, often gold-plating) to the program offices for solitary or joint programs. Some requirements are complementary, many are not.
The joint F-111 was largely driven by Secretary of Defense Robert McNamara, who as one derider noted "knew the cost of everything, and the value of nothing"
The jointness on the MV-22 Osprey (before the Army dropped out) was largely driven by a convoluted allegiance of senior DoD, congressional and industry partners. A later SecDef tried to cancel it, but got out maneuvered.
The Joint Strike Fighter (JSF) resulting in the F-35 was largely driven by Secretary of Defense Les Aspin, and was a conglomeration of a dizzying array of JAST, CALF, MRF programs to replace various US, UK and allied airframes. There has been general acknowledgment that the diverse requirements for the A, B and C versions compromised each one, and continued arguments whether two or three different aircraft would have been better off after all. While the F-35 is maturing, I cant help but think that it was over compromised.