Once you've handed off your paper ballot, it's no longer "transparent". You have no signature (physical or digital) that verifies that your vote was counted in the final tally. You also have no proof that all other votes submitted in that election were legitimate votes from real, identified eligible voters. Ballot stuffing and mis-recording of votes are both forms of fraud that have been performed under the so-called "transparent" paper voting systems...
"Accountable" implies that you have adequate identification. Last time I checked (last presidential election), I only needed to provide a name and a birthday in order to vote, which are both things that are publicly available information. Without adequate identification of people (see: biometrics + smart cards, ideally), you don't have accountability or even the ability to reliably detect voter fraud. Why would you want to favor a paper system which relies on people (who can be paid off, blackmailed) when better solutions exist that get rid of some of the possibility of human error?
Personally, I'd rather have a public electronic voting system where all voting transactions are stored on a public blockchain. That way I can verify the vote tallies for myself and I can also verify that the vote that I submitted was actually recorded and included on the public blockchain. You add in the assumption that all voting machines must be closed source and un-audited - but that's not an inherent property of voting machines. Governments could just as easily use open source and publicly-audited voting machines.