Okay, in this game, the villains are basically a cross between Cobra and PNAC and couldn't be more blatantly Conservative if they wore giant flashing neon signs on their helmets reading "I'm a Conservative." So why is it that in Empire, which was written to promote this game, the villainous organization "The Restoration" is suddenly the Liberal "Progressive Restoration"? It doesn't make any sense. Liberals can be bad, yes, but the rhetoric about restoring America to a Golden Age where it was the "greatest country in the world", and establishing an empire that will rival Rome is distinctly Conservative rhetoric, rather than Liberal or politically neutral.
Not to mention that this isn't nearly the only thing that doesn't line up. Reading a plot summary, for starters, the Vice President is killed in Empire simply by a dump truck backing into his car. We don't see exactly how the Vice President dies in Shadow Complex, but it involves an explosion, so it's not that.
Related to the above, why do they insist that Shadow Complex still ties into Empire and its sequel, when they're some sort of right-wing bizarro universe version of the Shadow Complex universe?
It happened because Orson Scott Card didn't write the game. Peter David would hardly agree with pretty much anything Orson Scott Card would have to say about politics; whether that's a good thing or a bad thing likely depends on if you liked the novel or not.
Those weren't in cold blood. All of the people he kills are either actively trying to kill him, or would if they had the chance — the law does allow for self-defense in cases where an immediate threat isn't present, but there is a persistent risk of harm or death; it's been used to clear abused wives who've killed their husbands, for instance. Lucius is unarmed and completely harmless aside from his ranting. Killing him would be in cold blood, even if it would probably save lives later.
Is killing Lucius even necessary- why can't the NSA agent arrest the unarmed terrorist, who would probably be more valuable alive?
Basically, because it's more dramatic to have her show up with a False Gunshot.
Early in the game, Jason gets to the helipad just in time to see Claire being thrown into a helicopter, which then takes off. He finds her later on, approximately fifteen minutes away on foot. Why did they need the freaking helicopter?
Carrying a person for what's fifteen minutes on foot for an unencumbered person through rough terrain is difficult and time-consuming. The helicopter made the transport quick and easy.
The vault where the Omega Armor was initially being stored bugs me. Ignoring the man-sized air vents since those are standard issue in fictional villainous hideouts, the front door to the vault is appropriately protected for such a valuable item - elite soldiers, energy barriers, unbreakable vault doors. So why the hell is there a giant unguarded hole right above the armor? You do have to sneak past two elite guards, but then you just drop in the through the completely unexplained hole in the vault roof and grab the jetpack, easy as pie. That has got to be the most absurdly obvious security flaw I have ever seen. Whoever designed that vault should be used as target practice.
It's so deep in the base that anyone unauthorized should be dead already. Emphasis "should be".
Why would they even bother guarding the suit at all if they were convinced that no intruder could get that far? It makes no sense at all to put so much effort into guarding the front door while simultaneously leaving a large unprotected hole in the roof of the vault.
Why didn't the Omega Armor Jason stole have an override switch built into it? The stolen suit worn by the Secret Service agent in the prologue was shut down remotely by a Restoration agent. If they built such a failsafe into one of their super-suits, why not all of them?
The most workable explanation is that the Omega Armor is still a work in progress and the suits of it we see are two ten or less in existence, probably with engineers still adding tweaks and smaller features to figure out the optimum load. Since everyone in the complex thought they were too well-hidden for any outside threats to find them, perhaps they never bothered installing one on that suit because they didn't see a need and wanted to spend their time on other things. It's insinuated that the armor we see the standard Restoration soldiers wear is itself a lesser form of powered armor (you can overhear two guards talking about it, one will even complain that he's tech-illiterate and has to have a buddy help him calibrate his own armor because it goes over his head.) If they were actually producing the Omega armor in any kind of numbers yet, you'd think you'd see some Elite Mooks wearing it.
Jason is only able to win because he steals all of the Restoration's advanced prototype super weapons to use against them. Ignoring why none of these devices had an override switch built into them, why didn't the Restoration just give all that gear to their best soldier and send him to kill Jason the moment the realized their intruder was a One-Man Army instead of waiting around for him to steal it all and become even more invincible?
They didn't realize it until it was far, far too late for that and he had already gathered most of said tech — notice that through nearly the entire game, they treat Jason as some two-bit spy who is no match for their training and equipment, and only start to take him even remotely seriously about the time they lock him into a room rigged to explode.
Except they should have realized it the moment he broke into the first omega suit vault and security system kicked in and moved the suit to a new vault, allowing Jason to just barely grab the jetpack for himself. There's even a cutscene of Lucius watching Jason over a security feed! So the Big Bad knows at this point that Jason is a serious threat, fully capable of breaking into their most secure vaults and stealing their most advanced tech, and that he must have killed several dozen soldiers to get that far, and yet he still doesn't take him seriously?
Lucius is quite clearly portrayed as supremely arrogant and not nearly as bright as he believes himself to be. It's not really out-of-character for him to continue to underestimate Jason for as long as he did, even if it wasn't wise.
Because that would be a really crappy game. How fun would it be to grab the armour and then immediately have a killswitch activated so you can't move and then a guard comes over and shoots you in the head, game over?
Also, they DO react appropriately: they send special units to find and kill Jason, including the ninja soldiers and soldiers in the XOS-1 power armor suits. And this is before Jason gets the full suit.