Yes but in the case of non-Alliance, non-Cerberus personnel the most he could say was "get off my ship", he wasn't in command of Wrex or Primarch Victus in ME3 or Tali or Garrus really. They could have disobeyed any order Shepard gave them without any other repercussions other than not being able to take part in the mission. They were not compelled to do everything Shepard said and their "careers" were never in jeopardy. If we're talking about power dynamics and abuses of said power, I don't think Shepard was necessarily in a position to do that with most of his squadmates. There is also an optional conversation Shepard can have with EDI, where she asks him point-blank if Shepard thinks it okay for a crew member to disobey a direct order that they don't agree with - you can either say yes or no depending on how you want to play your Shepard.
I have never been in the military so no, I do not have first-hand experience of how fraternisation might poison a squad or command relationship (as you put it). I defer to you on this and believe you when you day that in very many (probably even the vast majority of) instances where it turns out to be disastrous for all involved. What I don't believe is that in <i>every</I> instance, this is the case. And while you may think that Bioware is side-stepping the issue altogether and painting Shepard as the ultimate leader when you believe him to be incompetent, I would remind you that the Alliance Navy is not the US Navy or the Royal Navy or any other military organisation that exists in real life. There may be many similarities but the Alliance quite obviously operates very differently. The strict command structure technically exists but Shepard and his crew are basically given carte-blanche to do what they want and when restrictions are placed upon them, they just do what they want anyway because they do what they think is right, not what they're ordered to. Is this realistic? In our world, no. It would be utter chaos and people that go against orders are punished even if it turns out they were doing the right thing. In an idealised fantasy world, the hero risking being tried with treason to save the galaxy from themselves is what makes the polt compelling for those of us that enjoy such things.
You're repeating the regulation argument again.
Shepard doing whatever he or she likes despite any and all restrictions that would normally apply (or in an absence of them) is an example of why Shepard is often a bad leader, not an unrealistic one. Bias, favoritism, and ignoring rules are quite realistic. Just because the rules can't be held to you doesn't mean it's not bad leadership to go against their premise.
Now, I have no issue with slandering Shepard with the brush of bad leadership. There are and have been people who protested, because they want to envision their Shepard as the most awesomest person and leader of the power fantasy that Mass Effect nakedly is. Or they say it was all good because nothing bad came of it. To which I say... congratulations. Your bad leader got lucky. More power to you.
It's not that I expect Bioware to ever hit military fraternization, mind you. To date with Bioware, fraternization concerns have been a dramatic/excitement threat to add spice for a relationship, not an actual threat or something others would condemn.
But then, what would you expect? These are the writers who Shepard was a good character to throw a PTSD/war stress plotline at. And, for some reason, thought that the above would be a credible candidate for 'most respected war hero in the galaxy' reputation for all the military soldiers encountered. You know, because he was an officer 'in the trenches' and 'just like them' with hisher three hot meals, hot showers, and a bunk (possibly with pretty LI) on a stealth ship far away from the front lines with short missions and frequent shore leave.
Actual soldiers would eat Shepard alive. Forget the heroic return to Earth as hero of hope for the resistance: Shepard would be lucky if the resistance didn't snidely thank the Commander for coming back after leaving them on their own.
Or maybe they did, and Anderson was just running interference. Can't have those fans learning how big of assholes soldiers can be towards their favorite projection avatar whose supposed to be the best of the best. (Uh, yeah. About that...)