The 2000 presidential election is far enough in the past that we can see what its effects have been and will be. The specific voting problems (such as the butterfly ballots) have led mainly to moves towards voting using machines that would make it easier to be sure that one's vote is correctly recorded.
The more important change has come about because of the closeness of the vote. The two parties have moved to trying extremely hard to get out the vote in their own base and/or to suppress the vote in the opposition's base. We can see this most clearly in efforts by the Republican Party to require all voters to show photo identification at the polls. Because elections can often be very close in today's political atmosphere (as they were in 2000), the parties are very eager to ensure that they take any possible advantage to increase their share of the vote.