Replaying ME3 as I am, I got to thinking about some of the theories I had about the game when I was playing it for the first time. The twists that I expected to come as a sudden reveal, but which never happened. The two that stuck with me were: 1) I expected that Admiral Hackett was actually a fake, and 2) I thought that Cerberus was self-sabotaging as part of some grander plan.
For Hackett, it was something I noticed early: Whenever we spoke to him via hologram, we never saw him, only the projection. Starting in ME2 and continuing in this game, when we remote-speak to other characters the game perspective would frequently transfer to their location and show them looking at our hologram. The Illusive Man is the most frequent example, we would get to see the screens he was looking at, the other people in the room with him, etc. With Hackett, however, early in the game we never got that perspective switch.
When you couple that with the way the Alliance Fleet had been so severely decimated in the opening battle and Anderson even specifically mentioned that it was odd that they hadn’t heard from Hackett, I began to think “OMG, this is a computer simulation of Hackett, or he’s been indoctrinated and is in a Reaper facility!”. ....then one time it did switch to Hackett, and it showed him actually working on the Crucible, and I had to toss the whole theory out.
For Cerberus, I noticed that so many of the Cerberus-specific missions wound up not only with me foiling their plans, but they actually left the Alliance in an even stronger position afterwards. Many of them revolved around Cerberus researching some new technology or preparing a new weapon that we had no idea about, and then their location would be discovered just before they were ready and we’d come in and take it for ourselves. We had no idea about Javik until they dug him up (And left his pod suspiciously unguarded, too), they repaired a massive defense canon on Tuchanka, we found new alien-specific medi-gel at their research base that was studying Reaper tech, etc. Each time, their effort and work lead to a stronger Alliance.
Many of these missions are curiously staged, too, where the enemy forces don’t show up until after we’ve landed, as though they were waiting for us to find whatever is there and then popped up to say “Oh no we are too late you are escaping with our Super Duper Mega Canon I can’t believe you got it oh well”. Especially since there are a few key missions where Cerberus mounts a much more effective and intense defense, putting these other “No enemies appear until a single shuttle brings in two Assault Troopers halfway through” missions into a new perspective. I wasn’t sure why they were doing this, but I was convinced the endgame would reveal that the Illusive Man had some sort of plan for all these missions that counted on our involvement. ...and then we learn that his ultimate plan didn’t count on him losing any of these side missions and we really were just outmaneuvering and outfighting his forces.
I was so convinced that I had predicted these “twists” when I was first playing the game, and I was almost disappointed when I realized they weren’t twists at all.