This is why I love Penny Arcade -- calling the BS out.
They're making fun of Conviction's overly stupid and convoluted plot that makes no sense. I'm sure they'd have a field day with this newest trailer/gameplay.
I don't think it was the plot itself that was the problem, it was Vic's weird narration (which basically carried the plot) and I think that's what they're making fun of. A lot of things he said sounded dramatic until you thought about them and realised they made no sense.
Like saying that Sam's agency betrayed him and told him to shoot Lambert... the guy who wrote that obviously didn't play Double Agent.
Which reminds me, Penny Arcade also made fun of the story in Ghost Recon Future Soldier. I gotta go find the comic and upload it.