Shiraz is not bad stuff, you know...
Yes, it could have been argued that the right way to do it would have been to build three aircraft. The Marines could have dispensed with all-round stealth, since their core missions are CAS and defensive counterair, and would have a lighter and simpler aircraft; the AF would probably have ended up with a slightly stealthier, delta-winged design, maybe a bit like a stealthy F-16U; and the Navy would have had a son-of-A-12.
All sorts of parts, procedures and processes would have been common. It would basically look like the Airbus program, with common parts on all sorts of aircraft from the A318 to the A380 and A400M.
Unfortunately, the concept was way too sophisticated for anyone to sell it to the White House or Congress; and the usual Optimism Disease set in, in which if the Pentagon utters a requirement, nobody will say it can't or shouldn't be done.