Joseph Harrison said:
Except it states in game that it has been half a year since ME2 and it states in game that James Vega was guarding you as well as in a comic that was released. So that is how James knew Shepard before the start of ME3 that isn't a plot hole it is about as explicitly stated as possible without breaking the show don't tell rule.
Are you farmiliar with the "Hierarchy of Cannon"?
Everything that is relevant to the top tier (The source material, the games in Mass Effect's case) Have to hold up under the scrutiny of that tier alone. Any extended universe material can draw from (Or rely entirely on) the audience's understanding of higher tiers but not the other way around. So if Bioware decided to incorporate lower tier extended universe into top tier cannon they have to make sure that people who have only experienced the source material can pick up what's going on. (And if that means an exposition dump, then it shall be so.)
I'm not sure if what James said about Cerberus was a plot hole but that did piss me off.
ME1 Cerberus is bad
ME2 Actually no Cerberus is really cool and good and are just misunderstood
ME3 Scratch that Cerberus is bad again
Make up your damn minds Bioware
That's kind of taking presentation as fact.
ME1 The Alliance says Cerberus is bad, You have no reason to think otherwise
ME2 Cerberus says Cerberus isn't as bad as the Alliance says they are, You get to make up your own mind.
ME3 Bioware says Cerberus is bad and that they've always been bad and fuck Mass Effect 2
Facts are more like
ME1 The Alliance tells you to shoot up Cerberus facilities, then grounds your ship even though you're trying to save the universe.
ME2 Cerberus brings you back to life, gives you a ship and a crew and helps you save humans that the Alliance won't lift a finger to protect. They're not giving you much of a choice and they have ulterior motives but they're not hiding it from you.
ME3 They're attacking you, killing and experimenting on human refugees, orchestrating a government coup, and generally trying to stop you from saving the universe. And according to James they were helping the Collectors abduct the humans they brought Shepard back to stop.
You see how the first two are morally grey.
and see how the third one is completely morally black and stupid too.
The one thing that Cerberus, the Alliance and Shepard agree on is that Cerberus is out to help humanity.
So Killing and experimenting on humans, Stopping Shepard from saving Earth, and helping the Collectors abduct humans are all against The Illusive Man's MO.
(And if you want to use the "TIM is indoctrinated defense" He wasn't indoctrinated during Mass Effect 2 when he was supposed to be helping the Collectors abduct humans.)
So they might have been bad guys the whole time, but all the stuff they do in ME3 is directly against everything, The only thing they stand for.
Except in ME3 Anderson says that he resigned as Councilor and let Udina have the job because, as shown in ME2, he hated being a Councilor. Also I'm pretty sure that the original plan was to make a new council where Humans were the leaders of the council and the other councilors were just puppets that would do what humans say. Of course its been 3 years since ME1 so you can assume that humanity has lost a lot of political clot seeing as the prevalent anti-human sentiment in ME2.
In the same ME2 scene when he said he hated being a councilor he also said that... oh just listen
http://youtu.be/DbNNlOiPbPk?t=5m24s
"As much as I complain I have an important job to do here."
That doesn't sound like something somebody who's willing to throw in the towel on humanity would say.
My biggest complaint is that the total script for ME 3 was about one fifth the length it should have been.
If I (For example) Picked Anderson, Killed the Council, Gave Cerberus the Collector base and Rewrote the Heretics.
My playthrough of Mass Effect 3 should have nothing in common with a game that picked Udina, saved the Council and destroyed the Heretics and the Collector base.
The way it stands now Mass Effect 3 is a hastily thrown together cash in to capitalize on all the emotional investment that was devoted to the first two games.
The stuff they did throw together wasn't even good- retconns and plot holes aside.