Example 1: Approach to Madison St. James
Saint Thorson made super happy friends with Madison and boned her. Found our who her daddy was. Then she dies because he chose the bombs over her.
Douche Thorton did everything he could to piss her off. Eventually she decides "enough is enough", knocks him out using SUPER PLOT POWER, and escapes his safehouse. Despite this drastically different relationship between Thorton and St. James, Marburg still kidnaps her and uses her for leverage over Thorton during the bomb plot because...uh...lazy writing? I guess?
Example 2: Mudering SIE
Saint Thorson was friendly with SIE. This didn't change much besides making her a possible handler on the last mission.
Douche Thorton murdered her in cold blood after Brayko kidnapped her. This resulted in her...not being a possible handler on the last mission. Oh, and losing access to her items. The story was for the most part completely unaffected by this character's death.
Example 3: Approach to Albratross
Saint Thorton was super bro-y with Albatross and Sis. This resulted in...Albatross being a possible handler for the last mission. And not being a dick while talking to Thorton.
Douche Thorton did everything he could to piss off Albatross. Murder Sis? Fuck yeah. Remove the bug from his servers? Fuck no. Result? Not available as a possible handler for the last mission. That's it. There was even some implication right before the last mission that Albatross might attack the Grey Box just to get to Thorton because he pisses him off that much. However, nothing came of it. A shame, because that actually would've been sort of cool.
Example 4: Mina
Saint Thorton loved Mina, and Mina loved Saint Thorton. They were tight, got their sex on, and saved the world together.
Douche Thorton hated Mina, and Mina hated Douche Thorton. It's hard to blame her, considering her randomly gunned down CIA agents, NSA agents, local cops, civilians - anyone who got in front of his gun. And yet, other than some dialogs at the end, nothing changed, despite the fact she's your handler for a good 75% of the game, if not more. She doesn't even have added snarky VO up until the last couple of dialogs with her, to the point where it really felt forced when she calls you a "monster" at the end of the game, despite helping you on every single mission before this one and never trying to talk sense into you. Lots of missed opportunities here.
Example 5: The End Game
Saint Thorton snuck his way through the adventure, befriending everyone, then ended up taking down Alpha Protocol and riding off into the sunset with Mina, followed by the ridiculously half-assed "radio broadcast" ending that made me long for DA's ending slides.
Douche Thorton murdered the fuck out of everyone, then ended up taking down Alpha Protocol and riding off into the sunset with Heck, followed by the ridiculously half-assed "radio broadcast" ending that made me long for DA's ending slides.
These were some of the most notable things, for me. I could obviously analyze all the tiny differences between the playthroughs, but what it boils down to is this - the largest differences were what Thorton learned about the plot. Saint Thorton never learned about Mina being the reason he had to go rogue, and Douche Thorton never learned that Scarlet was an assassin. Beyond that, some changes in e-mail text, and the availability of certain items in the store and certain allies in missions...nothing really changed.
The best part of the game, I thought, is how characters outside of missions responded to your actions during the missions...but I don't think Obsidian took that far enough. For instance, Saint Thorton started off tranquing his way trough the Saudi Missions, so when he got to Nasri, he hadn't actually killed any of his men - but Nasri still accused him of doing so. A big deal? Not really, but gave me a glimpse behind the thin curtain that is the game's C&C.
Another example? How about the fact that at the end, no one seemed to care Douche Thorton had murdered his way around the world, except in a few pieces of dialog here or there. You'd think Westridge of all people would want a piece of him, but oddly enough only Saint Thorton fought him. This is despite the fact that the mission briefing for the last mission specifically says to watch out for traps set by Westridge and Darcy because they're all pissy about the murder-spree.
Overall, let's look at DA and AP when it comes to the ending and how much it changes based on player action:
AP: Thorton either joins with Halbech or doesn't. Either way, he has to take down AP. After that it's just a matter of whether or not Thorton is working with Halbech, and whether or not Halbech's role in everything was revealed. Really not much variation, and it all comes down to a single choice that you might not even be able to make unless you got buddy-buddy with Leland. The story is in more or less the same shape when it comes time for the hypothetical sequel-that-will-never-be.
DA: By comparison, this game varies a lot toward the end. Two of the most long-loyal companions can abandon you, or die, based on your choices. This isn't including other companions that can leave or even die before you ever get a chance to meet them earlier in the game. Based on other choices, the game ends with either the Warden heroically sacrificing himself, or Loghain redeeming himself by sacrificing himself, or Alistair sacrificing himself, or no one dies because a God-child was born instead. The Kingdom is then ruled by a cocky, heart-over-head young Warden, or an intelligent and perhaps a bit devious Queen, or the Warden himself, depending on other choices. In all these various endings, the story being told is subtantially different. In fact, I would (and have) argued that depending on how you play, the game can very-much play out as a tragic stroy about Loghain's fall and redemption. If you play another way, Loghain is just a whiny little cunt that gets his head cut off by an even-whinier cunt-who-would-be-King. I don't think there's anything nearly as drastic, story-change-wise, in AP.