Shoggoth2588 said:
When it comes to Mass Effect, how did Udina end up as the Human Councillor in ME3? How did Anderson get ahead of Shepard in The Citadel at the end of ME3? Finally, in ME3 as you're making the final dash towards the Citadel Beam thing, what happens to your party? Personally, I kept Garrus and Liara with me so they should have been killed by The Reaper beam and yet we see both of them safe and sound on The Normandy...Tha Hell?! None of those plot holes ruined Mass Effect 3 for me since they're minor when compared to the awesomeness that is Kalros vs Reaper and certain other character moments.
The biggest plot hole for me was also the simplest.
Anderson: "Our objective is to reach that giant beacon, which the Reapers now control. It'll be a slaughter, but if we can get even one man inside that thing, they'll be able to activate our magic (Deus Ex Machina) super weapon and destroy the reapers forever. Any questions?"
Me: "So why don't the reapers just turn it off...."
Just like that the magic was broken. I still loved the game, but the whole time I kept hoping that the writers would explain the plot hole. Maybe this was just another layer of control. Maybe Shepard was indoctrinated, and he was supposed to lure the entire Allied fleet into one place so that the Reapers could destroy them in one fell swoop. Therefore, the Reapers wanted you to reach the beacon the entire time. After all, Bioware had great writers. They knew what they were doing. Obviously... that's not what happened.
Also, anything David Cage related. It's not uncommon for games to have poorly developed stories, but if the story is the entire crux of your game, and if you're going to play tortured artist, you better make damn sure that you have all your ducks in a row, because plot holes are unacceptable. Heavy Rain was interesting, but the shamble of a story and the rapey bits destroyed the entire game for me. For someone focused on video game story telling, David Cage is a really poor writer...