You are assuming a LOT of things either not in evidence (that MC has the slightest clue about subtly tampering with supply chains), that are actively contradicted in the story (that The Company is the Org's only supply chain point when we know the Marina at least was another one) or that are factually wrong (MC out on a personal quest for revenge to find the person responsible for what happened to his mother has to lead to WAR).
There's a lot of other points that could be gone into where you've misunderstood MC's motivations (investigating vs toppling shadow empire) and think he should be behaving more like a spec-ops commander, or have gotten aspects of the geography and suchlike wrong (the tunnel doesn't lead into the city), but everything salient is covered in my original post.
In short, everything comes down to the question of: did the MC behave in a way that is believable for his character as demonstrated throughout the game? I would, of course, argue yes (he's got a certain amount of cunning, and adapts quickly to new situations, but he's also kind of a dummy). If you disagree then that's a shame and I hope you can look past it and enjoy the game regardless. If not, that's okay - it's impossible to please all of the people all of the time, and fortunately there are so many awesome developers working in this field that I'm sure you'll find something more to your taste.
In any case, for any further questions on this topic, I refer readers back to my original list so that this doesn't turn into a one-hundred page dissertation ;)