To be specific about Flanagan's points:

The foregoing is an example of what William James called the philosophy of "nothing but." Its practitioners can be counted upon to reduce any phenomenon, however mysterious, to: "O, that is nothing but (blah blah, quack quack)."

Discussed in several places on Overcoming Bias. In this sequence, mainly Quantum non-realism. But also Fake Reductionism and Angry Atoms.

Closer to home, Gell-Mann has recently opined that Bohr & Heisenberg "brainwashed" a generation of physicists into thinking QM was complete.

Quantum Non-Realism, If Many-Worlds Had Come First

"But where does yellow come in? he will say: In my picture not at all, but these kinds of vibrations, when they hit the retina of a healthy eye, give the person whose eye it is the sensation of yellow." (Schrodinger)

Where Physics Meets Experience

"It seems clear that the present quantum mechanics is not in its final form [...] I think it very likely, or at any rate quite possible, that in the long run Einstein will turn out to be correct." (Dirac)

Einstein was correct. Spooky Action at a Distance: The No-Communication Theorem

"Anyone dissatisfied with these ideas may feel free to assume that there are additional parameters not yet introduced into the theory which determine the individual event." (Born)

Bell's Theorem: No EPR "Reality".

I realize this is a long series, but in the name of all cute kittens, don't tell me what it doesn't address until you actually read it! For the love of Belldandy, Montressor! This is a medium-sized book we're dealing with, designed specifically to reveal quantum mechanics as non-mysterious! Does it really not occur to you that these points might be, oh, addressed?