This spotlighted old problems in the election systems that were ignored when the vote wasn't so close. Hanging chads and misread punched card ballots have been around for thirty years. Bad ballot design has been there forever. Granted, close local elections were often decided by such problems but no one paid attention. The close election put unprecedented pressures on the accuracy of the ballot counting.
All voting methods have a margin of error.
Punched card ballots caused the controversy in Florida, but they were originally chosen for their speed and accuracy. This means that we will never really know who won the popular vote for the entire nation. Even hand recounting became controversial. In the old days when an entire ballot was counted by hand across an entire state, hand counting was highly suspect. Many people handled the ballots with all the potential for human error and cheating that this implied.