I get why Daniel would want Joanna to break into Area 51 to rescue Elvis, but in the meantime, why couldn't he have sent someone else to warn the president that Trent was trying to kidnap him? Are Joanna and Jonathan the only two agents in the institute?
Maybe they're the only agents qualified enough or the only ones available.
If we are to accept everything in both console games as canon, then since joining the Institute, Joanna has adoped an english accent, been labeled "inexperienced" (despite the fact she used to be a bounty hunter and defeated a "god") and forgotten what Jonathan looks like.
And Carrington has decided to ditch the kilt.
Well he doesn't ever look comfortable in that suit, does he?
The perils of next-gen consoles. I'd like to assume Rareware weren't even thinking about the original game when making Zero.
I can agree with you on everything but Johnathan. From the cutscene in Perfect Dark in which you meet him, it seems more like they do know each other, it's just that Joanna was still in "shoot everything that exists" mode, and Johnathan startled her.
No, in the original game, she comes upon a mook that she clearly thinks is Johnathan before Johnathan reveals himself.
Undercover agents can be wearing all kinds of disguises.
The game doesn't refer to the undercover agent as Jonathon until the mission briefing in Area 51-Rescue. Joanna just doesn't recognize the voice, which has changed just like Joanna's voice has.
It bugs me that the RCP-120 can hold 120 bullets in what doesn't appear to be a very big clip. Still an awesome gun though.
If you can accept a gun that uses mineral bullets which it converts into a light-bending cloaking device, then frankly that's the least of your worries.
I can understand that the Skedar are using holographic generators to make themselves appear to be a human under the name of Mr. Blond... but what I don't understand is how in the G5 building mission, Mr. Blond was sitting down in a chair, when a Skedar Warrior would be incapable of sitting in the chair.
What bugs me more is that, if I recall correctly, they stay in their Blonde disguises when you kill them in the Crash Site mission. Avoiding spoilers, sure, but unless their disguises aren't lifeforce dependent ...
It bugs me that his name is spelled "Blonde". It's clearly an alias, but they could at least spell it correctly, considering he's (supposed to be) a man.
I guess to the Skedar, all humans are the same, so why would they concern themselves with something as "trivial" as political correctness??
Carrington doesn't seem like such a swell guy when you think about it.
Initial Vector portrays him as a man at war against dataDyne and the MegaCorps, and is fairly jaded, cynical and ruthless. Plus I might be mistaken, but those after Jo I believe were NSA agents with Trent and the snow guards and Presidential security are rank and file US employees. The guards won't go after you when you are face to face with the President, and they'll go off and fight the invading NSA if spared. Area 51 though, that is morally ambiguous.
Why do weapons like the Tranquilizer and Crossbow, both with an instant-kill alt-fire that does just that through chemical/poisonous means, take down an energy shield in one shot?
Same sort of justification as the battle droids in The Phantom Menace being able to penetrate the shield, but not their energy weapons. Lasers and bullets are compact and travel at supersonic speeds, so the energy shield is specially tuned to be able to cancel out the damage they impart, at a cost of a fraction of it's own energy supply. But a crossbow bolt is long and is fired at subsonic speeds, so the shield isn't designed to be able to stop it and if it's lethal, it will still hit the person and execute them. On the other hand, the lethal injection overdose of drugs depends on delivery mechanism-skin contact and the shield isn't able to prevent people and other macroscopic objects to come into contact. It makes sense; if the President wore one, fine he's protected but the shield still has to let him shake hands with other politicians and go about his daily life with as little inconvenience as possible.
Why does the RCP-120's cloaking device use bullets as fuel, to the point of using the ones in the next clip right when the reload animation begins, all through the time you finish reloading?
Simple: the in-universe discovery of cloaking technology required Applied Phlebotinum in the form of rare mineral bullets, which also happen to be on par with regular bullets in terms of lethality. Obviously the specifically designed cloaking device uses the mineral but in a shape/form that can't double as ammunition. They can afford the RCP-120 a short residual charge, long enough for a skilled user to do a reload in a short space of time and allow the next magazine/effective battery pack to carry the charge on. The designers recognised that unless the user specifies otherwise, they'd probably appreciate being able to stay invisible rather than suddenly (and inconveniently) appear in the middle of a hostile area.
Why does Joanna have to activate the autoguns herself in the Carrington Institute? There are guards placed all around the lower levels who could do it for her.
The guards are competent at point defence, but Joanna is the only agent immediately to hand and in general, the only person skilled enough to both engage the enemy and activate the autoguns. In-universe, their computers might require a bit of programming know-how, which grunts wouldn't be trained for. Also, the enemy deployed energy shielding and K7 Avengers and brought a Skedar along to play. Only she could have swept from room to room and had a hope of surviving.
Joanna is surprised to see that Cassandra's been captured as well, to which she replies "there's no hiding from the Skedar". She was hidden so well in her office...
She didn't mean that she literally went into hiding, but she was entrenched in dataDyne HQ with her female bodyguard private army, a Dual Wielding captain and specially trained male guards equipped with magnum handguns and N-Bombs. She didn't think even the Skedar would be able to penetrate those defences, at least not without her being able to pull a hasty getaway. Joanna claims that the Institute "found no trace of her", so perhaps she was actually hiding very well but decided to return to HQ that night to retrieve something with her army. Unfortunately for her, Skedar military intelligence was just too good.
If the Skedar really are supposed to be mechas, as unlockable material implies, why do they bleed when shot?
The fluid is a mechanical analogue to blood which controls various functions within the mecha. It just happens to be the same color as the tiny/"true" Skedar's blood, for whatever reason.
Why is it that when the Skedar aren't disguised as Mr. Blondes, they are almost impossible to knock unconscious with your fists, but when they are disguised, they get knocked out just like any actual human?
The hologram simulation technology runs more than just "skin deep"; it perfectly replicates the human physiology with all of it's strengths, limitations and vulnerabilities. Your Mind Makes It Real and the shocks that a Skedar could shake off are lethal when they're impersonating an Earthling. So Blondes (unlike Terminators or Agents from The Matrix) are constrained to run at the normal speed of a human being, have the same strength and are as vulnerable to bullets and fists as an ordinary person (or elite Nordic bodybuilder, take your pick). Why didn't the Skedar make them more durable you might ask? Either the technology was constrained to having to simulate exactly, or they just didn't take it into account.