You know who suck? Nazis. You know who are incomprehensibly evil? Nazis. You know who plot the destruction of humanity? Nazis. You know who probably need to have their asses kicked by anyone with free time and maybe a star-spangled shield? Nazis.
There doesn't need to be a guy in a weird mask with strange and vaguely supernatural powers, with his own special cell of crazy workers. The entirely mortal and terrifyingly bureaucratic malevolence of the SS is really bad enough, and I will cheer at least as much when it is defeated.
Maybe it's off-putting to have that kind of not-at-all cartoonish villainy in a comic book or comic book film, but, in a strange way, having HYDRA be the motivating force behind various Nazi plots cheapens their real barbarity.
And actual Nazis can be after the Tesseract; they just have to walk the right side of the Indiana Jones line. It would still make a good movie. JJ Feild and his cute red beret can come too.