Same director, so similar in style at times. That's where the comparison stops, though.
I like 2049 better. Part of that is I'm just a much bigger fan of the Bladerunner franchise and its themes interest me more.
I never read Dune and only watched the original early this year, in anticipation of this new film coming out.
Comparing Dune to Bladerunner 2049 is like comparing Dune to Arrival or Sicario, simply because it's the same director.