The two fundamental questions to me are the WHY and the WHEN.
Why would Mofftiss feel the need to tell their story in this particular way? They said that it's a show about a detective, okay. But why would they feel the need to tell the story (or parts of it) in Sherlock's mind? What would be the advantage of that? And furthermore: Why would they do this in such a cryptic way? Wouldn't they want to have the whole audience, fans and casual viewers, on board for the ride? Wouldn't they want everyone to get it? What's the use if a large part of the audience doesn't even get it and just thinks that something is weird and feels a bit off? Wouldn't there be more obvious hints? Or am I supposed to believe that to Mofftiss it's okay if some people get it (and not even immediately but only after lots and lots of metas have been written) and a large part of the audience just thinks that things don't really make sense.
I am willing to believe that something like the laptop scene in TSoT is indeed MP and that it's okay for the writers that not everyone understands what's going on in that particular scene. But seriously, doing MP on such a huge scale since HLV (or whenever this is supposed to have started) without giving more accessible hints and running the risk of 90 % of the audience not understanding it... I simply don't believe it. It would be too clever and too stupid both at the same time.
And the WHEN: When exactly did we enter Sherlock's MP and when can we expect to get the resolution? In five years maybe, if we do indeed get more episodes? Or maybe never? Even if it would be in five years, what kind of story-telling is that? Again, the casual viewer will long have forgotten about the details in TFP or even HLV. Or did we already get the resolution in TFP and most of us have just missed it, again?
I totally understand the need to understand what we have seen and to make sense of the inconsistencies. And it's a pretty deflating thought that most of it might indeed be due to continuity or other errors. But to me MP is not the answer. Mofftiss are pretty amazing writers, but maybe only most of the time and not always. I'm not even saying that they wrote themselves into a corner, I'm just saying that if they had given us three or more episodes in Sherlock's mind, then they would also have given us more distinct clues.