Wholeheartedly (or maybe downheartedly?) agree with this - sometimes I try to say the simplest things and people just stare at me like I'm speaking Martian. Which I suppose I might as well be! One of my big problems is implicit use of tones for things like expressing uncertainty; that's a very difficult habit to get out of.

Another one that I wish I had realized sooner is that, contrary to the impression teachers tend to convey, tones aren’t just a pitch contour thing. There are also intensity and cadence elements. Native speakers can fairly accurately recognize tones in recordings that have had all the pitch contour autotuned out.