"suddenly have the power – literally at their fingertips! – to turn other things 3D; brain-mushingly idiotic."
Actually this isn't quite what happened. They could turn things 2D (which was central to the plot) and also turn them back again. Crucially they could not turn 2D things into 3D things, hence how Clara saved the day.
Having said all that the monsters were developed way too fast. They could have explored a lot more what they could do as purely 2D monsters (perhaps as a two parter) before they became pretty generic baddies.
It's hardly strange that Missy's bit feels tacked on, after all it was probably a bit that Moffat added to Mathieson's story. Although it is strangely reminiscent of purgatory from Being Human. I like these overarching story lines, but they don't seem to be weaved in to the episodes as well as in the Amy Pond era.