A good balloting system should be designed in such a way that every ballot cast will permanently alter some medium in a way that cannot be altered or substituted without detection, and which can be examined without 'breaking the seal'. It should also be designed so that any type of malfunction can be detected immediately.
Paper ballots are actually not all that good in this regard, though the optical-scan ones are probably better than the punched-card ballots. All of those forms of medium have the problem that the seal on the ballot box must be broken to count the ballots, and once the seal is broken there's no way to detect substitution of bogus ballots for good ones.
Probably the best approach would be to modify a mechanical lever-action voting machine so that all of the counters count up only (i.e. they cannot be reset), they have enough digits to prevent them from ever being overflowed/"wrapped", and so that any combination of votes will cause the same number of counters to be incremented (i.e. in a "vote for one" race, there's a "none of the above" counter which gets operated when applicable, etc.) Additionally, the machine should have windows constructed in such a way that a voter who wishes to watch for such things can actually see the proper counters getting incremented [only the input shaft of each counter would be visible, and it would make one full revolution to register a count, so nobody who wasn't watching the counter getting incremented as it happened could see that it had done so].
Unfortunately, I don't know that this country still has the technology needed to produce such a machine at a reasonable price, and I don't really like the idea of "made in China" voting equipment.