Nothing a few thermal clips can't handle. That's a little bit of a joke, but not entirely one. My first instinct about Miranda was to shoot her; my gut instinct about the Illusive Man is even worse. The plot seems more forced than it does natural.
I hated it too. But I also accepted that nobody else was going to do anything about the Reapers so I (thinking in character) made the enemy of my enemy, my temporary ally. Realistically, in that situation, Shepard is pretty much at the Illusive Man's beck and call IF Shepard wants to fight the Reaper threat. Shepard might be powerful, but he'd be no match for Miranda, Jacob and the rest of the Normandy crew.
Keep playing, though, as you DO eventually get the option to stick it to Cerberus and the Illusive Man.
Another issue I'm having right now is feeling as though the second game doesn't really connect very well to the first game. Most of the characters I found interesting or had a connection with have little or no part in the second game; a lot of things are left unresolved.
Just how far have you played into ME2?
I ask because you do connect with most of your old team. Garrus and Tali can be squad-mates and Wrex is just busy. And, well, Kaidan/Ashley are just uptight PITA anyway so good riddance. And Liara gets a whole DLC, which is highly recommended, devoted to her.
A few plot holes bug me a little too.
Like?
The main complain about the game is feeling as though choices along the way did not matter as much as they should have.
The funny thing about this complaint is that it's only valid if you view the series as a video-game and not as a series of events in the life of a living, breathing person. As a video-game they're right, his choices mean very little and have very little impact on the story before or after the final choice. And that final choice is virtually meaningless under that light.
But if you view it as something 'real', then the fact is that no other choices could've gotten him to that conclusion. All the character's choices up until the final choice are the only choices that could've resulted in success, because nobody and nothing else has been as successful as this character in fighting the Reapers. So the character's choices were vital; if the character had gone left instead of right, the character wouldn't have made it to the Star Child and the cycle would once again repeat.
But people can't see it that way because they ARE the meta-game. They exist outside of those choices and know that regardless of what path they took, it would end up the same. They want realism for the character without accepting the reality of the character.