You list plenty of specific problems with GPG the UI and GPG the "API" (though frankly the fact that mailpile would write 1400 lines of python that wrap GPG rather than taking one of the independent library implementations of RFC4880 and bringing it up to production quality makes them part of the problem). But none of those specific problems are problems with OpenPGP the protocol.
Well, I was only quoting the article, but it sounds like he has a good point that the protocol doesn't support forward secrecy. I also tend to trust his judgment that it's too complicated, and/or the complication adds little value for "normal" users. I guess some of this can be isolated as an app/API problem rather than protocol, as you say.
Perfect forward secrecy is of course better than not, but I'm not convinced it actually helps a lot for realistic threat models. It means that when you utterly screw up and reveal today's treason you won't also be revealing last week's treason - but for someone who's using crypto for serious reasons, how often is it that last week's message would get you in trouble and today's message is innocuous?
Would a ground-up rewrite of OpenPGP have PFS? Of course. Is the functionality important enough to justify a new protocol? Not on its own, IMO.
