The problem that both the A-12 and the F-117N had in common was that salt air and radar-absorbent materials didn't mix. One assumes that those issues have been solved with F-35, though.
The Navy would've been better off if they had simply gone ahead with the A-6F program in the first place or reactivated it after the A-12's cancellation.
There was also the A/FX program, which envisioned a joint Navy-AF strike aircraft to replace the A-6 in the Navy and Marine Corps, along with the F-111 and F-15E in the AF. Canceled by the Clinton Administration in 1994 and JSF substituted.
The Lockheed-Martin A/FX entry: