"This seems like the best system to me. Most Americans are very familiar with bubble forms and there is a clear paper trail while still allowing electronic counting."
The problem is that the paper ballots may never be hand counted if the margin between the candidates given by the electronic vote counting machine is far enough apart.
Of course, whoever hacks a vote counting machine can give any vote count they want, so they can set the margin however wide they want.
The only way to really be sure of the totals is to do hand counts of paper ballots, with representatives of each party participating or at least observing the entire count.
Machines should never be trusted.