> A fix I would consider is to have the inputs more thoroughly checked for correctness before passing them on to the ATC system.
Thoroughly checking of the inputs as far as possible should be a given, but in this case, the inputs were correct: while the use of duplicate identifiers is considerably less than ideal, the constraints on where that was permitted meant that there was one deterministically unambiguous parsing of the flight plan, as demonstrated in the article. The proximate cause of the problem was not in the inputs, but how they were processed by the ATC system.
For the same reason, multiple implementations of the software would only have helped if a majority of the teams understood this issue and got it right. I recall a fairly influential paper in the '90s (IIRC) in which multiple independent implementations of a requirements specification were compared, and the finding was that the errors were quite strongly correlated - i.e. there was a tendency for the teams to make the same mistakes as each other.