The character range for Shepard, as written, is one who, regardless of not having to follow orders, still feels some sense of respect for the individuals in the Alliance to whom he/she used to report and some sense of remaining loyalty to the Alliance. Even a Renegade Shepard still shows signs of respecting the uniform and individuals like Hackett and Anderson. Hackett makes it quite clear at the beginning of the Arrival DLC that Shepard would be doing this as a favor to him not as an order from him. The player is not given the option to tell Hackett to just blow off (i.e. to effect end the friendship). This is essentially the same as the situation for much of ME1, where, I believe, you really only have the option to turn down Hackett once - that being the Beseiged Base mission where the dialogue basically tells Hackett that you don't have time for it and it results it you not receiving the mission.
For the most part (panty flashes aside), the options are entirely consistent with the range of characterization we've been given... one who respects the elder Hackett and Hackett's status in the Alliance. For example, people meeting elder people with stature - Drs., Officers, etc. do generally show these individuals respects despite not being directly obligated to "obey" them. Some people don't...Bioware has characterized all degrees of Shepard as the former... the latter is outside the parameters of the game. As I said, I would not have even blinked if there had been a "romance" option for a Femship to flash Hackett... but Hacket was not a "romanceable" character. The pany flash was really just poor execution of a cutscene on Bioware's part.
Despite your assertions that "player agency" and "player control" are two different things... it seems to me that what you really want is more "player agency" - i.e. the ability to just do whatever you want... i.e. to effectively "write" your own character. It's certainly does not seem to be just about predictability and "player control" with you.
The game asks me to make decisions on behalf of the character. Those decisions need to be based on something, so I invent personality on which to base those decisions.
This only works if I know to what parameters that personality needs to conform. But I don't, because the game doesn't tell me until it's too late.
I don't mind having my creatitivity constrained, but I need to know what those constraints are or I'll just run into them after the personality is already formed (and has already informed past decisions).
If I'm to roleplay this character, I need an in-character justificationfor every single thing she does, from what equipment she uses to what skills she learns to what missions she accepts and how or if she chooses to complete them.
Every time I create that justification, it needs to be consistent with all other actions that character will take in the game. Not every action she can take, but every action she does take. Therefore, if there are mandatory actions (such as following orders), we need to know about them so as to avoid creating justifications which preclude them.