Funny how people like to try to create themselves in the protagonist(not judging). There is a reason why in the previous games the hero was called Shepard and not the name you chose. I myself like very much the paragon version of Shepard. All those choices to this point has only been choosing Shepard's personality. The game would be really complex if there were more than good, evil and neutral options and would probably result in broken script.
I do agree though that there should be separation in what you are able to do with your current resources and time like in ME2 if you were't aware that you could save your crew only going right away. All of the loyalty missions were to only remove comrades hesitations on the suicide mission and not about results(overall).
It would be great though if there is future loyalty missions that the results are harder to accomplish. Like certain information, connections and charm. The charm and intimidation options power and consequences should be greatly reduced in this case and should not affect that greatly what kind of a person the protagonist is.
So yes I would like to see more loyalty missions. After all these are great way to bring more background to the story. Does not matter if these are main or side quests.