To a large extent I agree with what you said about the trend as well as Star Trek's current creators.
I too have had issues with Tonto and when I heard about Shredder. As for Trek one of the things regarding Khan which made me scratch my head was that up to this point Abrams-relatively speaking-has been okay with me with the casting of nonwhites in many of his films and TV shows. To be honest my expectations for Hollywood aren't that high when it comes to the development of nonwhite characters, main or supporting, but there are times when Abrams has exceeded my expectations.
Many of the black characters on Alias, for example, were more than one-note and I will always have a soft spot for Undercovers. And he has arguably elevated Uhura to third pillar status, even if I don't care for how he did it, in the Trek films. And he has given Sulu some badass moments-though not enough. It doesn't mean that Abrams is perfect or beyond criticism or could not do better, but I do think he gets it a lot more than some of his Hollywood contemporaries.