I agree with the fact that having a third time nazis in an Indy movie would have been too much indeed, and especially if the movie is set in the 50s, when the idea of "latter-day nazis" would have sounded really absurd and forced.
By the other way, I must admit that the choice of Ruskies is very well made: in fact they could think to a great enemy (Russia was the other power of the world that time) who has got an own army and who moves in uniform commanded by a insanely bad boss... The goodness of the choice seats not only on the circumstance that russians are, for their own characteristic, really interesting villains, but depends especially on the fact that substantially.... they are the same cine-type of the nazis!
That's what make "Mutt Willams" joke even more sensed, other than hilarious (although I sincerely hope not to hear any joke of this kind in the movie: too self-referent and reductive)!