As noted, the shotgun sequencing wasn't any worse than the traditional chromosome walking method used by the other human genome project, and neither created a truly complete sequence, which is only possible today with improvements in technology.

And it is worth noting that despite all the critiques of shotgun sequencing at the time as "cheating", chromosome walking sequencing is dead, and shotgun is what we use today. If anything replaces that it will be long read technology like that done by Oxford Nanopore sequencing, although we aren't really there yet (you still need to assemble that data and don't really get end-to-end sequences yet).