I agree! A heavy-handed use of brakes can be annoying and distract from the experience/show.
But in my opinion, the standard should be just that–experience and show, not the Coaster Enthusiast's typical litany of "better coasters" from around the world. If Disney is wanting to use brakes to, slow the train in order to create a beat for riders to see set pieces or better experience an effect, that's not necessarily a failure simply because "Mako and Steel Dragon..."
In other words, it's not that Disney uses brakes to slow the train mid-ride that's the problem. It's how the use of brakes affect the show/experience. To me, the standard is what Disney could have done, not what Six Flags does.