The nice things about the mark & scan systems are that the voter gets immediate notification of an unscannable ballot: stray marks, mis-marks, overvotes, and similar issues are correctable in real time by the voter, perhaps by exchanging the spoiled ballot for a new one, and destroying the spoiled ballot. The scanned paper ballots are also available to be rescanned for a recount or audit.
Creating a voting system for a many-race election that is intrinsically resistant to manipulation is harder that it first appears. I used to (circa 2000) think that electronic voting would supersede paper ballots in a few years. Now I think that paper ballots have a simplicity and durability that outweighs the apparent convenience of electronic approaches.
source: elections official in two states, voter registrar in one.