Making --wait the default may or may not be sensible -- I'm not sure -- but removing --no-wait is clearly a bad idea, and we shouldn't do it. The fact that the problems created by removing it might be solvable doesn't mean that it's a good idea to create them in the first place.
I agree with Robert - pg_ctl is no doubt used in all kinds of scripts that would then have to change.
It may make sense to have --wait be the default though - certainly less confusing to new users!