The single most egregious thing about the sc2 history is what they did to Mengsk.
In SC1, Mengsk is a really interesting character. He is introduced as the rebel leader in an evil regime, someone you ideologically align with. Then he's shown to be somewhat of a ruthless pragmatist, but very smart. Then, it turns out he puts selfish interests above altruistic one as he names himself emperor.
But even then, he's never the villain. He's just an asshole. The zerg are the real enemy, and then the UED comes and fights Mengsk (a battle where neither side is good, pretty sure there is no such thing in SC2), and he gets demoted to an asshole who doesn't even have power anymore. then Raynor saves him because they need his help to fight the UED. Here's how Raynor talked to him during campaign VI
And even once he gets to be Emperor again -- who cares? I never expected SC2 to be about overthrowing him. Why would Raynor give a fuck whether he's emperor or not? If he had worked with Mengsk, that would have made at least as much sense as trying to rebel against him.
Making him the arch villain is just so stupid
But at least in Campaign VII, that was the side plot; the main plot was about Kerrigan. Making him the arch villain in Campaign VIII is worse still.