Nicholas II's 'malleability' is in my opinion also a bit of myth.
Very true.
I think the source of this myth was the ineffective way in which Nicholas handled decision making. Any good corporate executive understands that all "stake holders" should be present when key decisions are made, so that all views can be put forward and countered in the open and then, when the decision is handed down, everyone knows what it is and which arguments prevailed. Then, agree or not, everyone leaves the room more or less on the same page about what is to be done next.
Nicholas preferred sequential rather than parallel debate. One minister would come in and make the case, say, for a new railway line. Nicholas would agree. Then the Finance Minister would come in and point out the difficulty of funding the project or the Foreign Minister would come in and point out the implications of the route from the perspective of some foreign policy concern, and Nicholas would reverse the decision. Meanwhile, the first minister had put things in motion for the project. He then later finds out the decision was reversed. Not only must he try to figure out who made the argument that prevailed and why the argument prevailed, but he appears chopped off at the knees in front of his subordinates, thereby undermining his authority.
It was this kind of subtle but perpetual chaos around imperial decisions that so frustrated Nicholas' ministers and that caused stories to spread throughout the bureaucracy of the irresolute or even duplicitous tsar. Different reasons have been given for this way of operating, but the one I find most compelling is that Nicholas was intimidated by the presence of greater intellect. It showed up in his silence when hard cases were put to him with strong argument, in the utter insipidness of his diary entries, in the choice of his entertainments, and in the astonishing mediocrity of the ministers to whom he turned as the wheels were coming off the cart from 1915 onward. And a person saddled with such intellectual limitations would find it much easier to mask that limitation -- at least to himself -- in one-on-one dealings with ministers rather than putting himself in the middle of a debate where strong and informed views are being exchanged in an open forum he is expected to control.
But, as you suggest, Vanya, I don't think this was malleability in the conventional sense. Perhaps because of the way it ended, even historians tend to look at Nicholas' reign too much through the lens of his personal life. And that lens homes in on his susceptibility to his wife's constant importunities, which was very real. But it diminishes the significance of a very important accomplishment Nicholas pulled off against the odds and against the desires of many influential constituencies -- the restoration of virtually total autocracy within a few short years of 1906, when most observers thought constitutionalism in some form had finally been made a permanent feature of Russian monarchy. In fact, your own argument that Stolypin was appointed to be Nicholas' pit bull in this mission shows that Nicholas could make clever choices in pursuing goals that really mattered to him. Say what one might about Nicholas' weakness and unsuitability to rule -- and I say more than most here -- this accomplishment cannot be overlooked or overestimated.
The Stolypin / Alexandra dynamic is very interesting in what it illustrates about the interplay of decisiveness and indecisiveness in Nicholas' character. For a long time Nicholas resisted intense pressures to remove Stolypin as reactionary interests came to realize that Stolypin's strategy for making the reimposition of full autocracy tenable was built around a reform agenda. But, in my view, it was Alexandra's unrelenting bedroom campaign against Stolypin that finally brought Nicholas to abandon the strongest ally he had in trying to keep autocracy tolerable to a Russia quickly evolving into a state of perpetual foment.
Its the double standards that get me, people are so willing to sympathise with Alexander III seeing his father die (in admittedly horrific circumstances) and to make allowances based on that for his entire reign but completely unable to cut Alexandra any slack what so ever for transgressions that pale into insignificance when compared to her father in laws.
I haven't seen too many people excuse Alexander's entire reign based on his seeing his father die, nor do I think that had much to do with Alexander's reactionary views which were formed long before 1881. Alexander III's dislike of his father's policies was well known to the father, to the point that there was speculation that Alexander II was toying with the notion of bypassing AIII in the succession. There were even some rumors that upon AII's drawing his last breath, AIII hurried to his father's study to retrieve and then destroy a document from his desk that took AIII out of the succession.
Whether true or not, such rumors indicate a widespread understanding even before AII's death that the son was going to be a very different commodity from the father as a tsar.