In the second game, the playable Venom is obviously Mac Gargan, not Eddie Brock. So how come in one level of the Wii version you battle both Venom and Scorpion, who is... Mac Gargan?
The absence of characters like Ghost Rider, Doctor Strange, Elektra, Blade, Moon Knight, and the Silver Surfer from 2 actually makes sense from a narrative perspective:
Because the Illuminati were Adapted Out, Doctor Strange has no real reason to get involved in what seems like a rather petty squabble when compared to the stuff he gets involved in as the Sorcerer Supreme.
The Silver Surfer probably helped Thor fight Galactus between 1 and 2 and is still likely helping clean up after the fact.
Since both sides are somewhat morally suspect (Captain America is technically breaking a law and Iron Man is straight up mind controlling people), Zarathos and by extension Ghost Rider probably concluded neither side deserved his help and went off to help people who he deemed actually worthy.
Elektra is an assassin for hire who repeatedly states how she doesn’t like getting caught up with big league superheroes in 1, so she probably went into hiding.
Blade usually only hunts vampires to begin with, and since the Civil War is not about vampires Blade has no real reason to get involved.
Moon Knight is both incredibly brutal and completely insane (he literally cut a dude’s face off), and whatever side recruited him would get a black eye if they recruited him, hence why neither side approached him.
It should be noted that Blade at least, is a playable character in the PS2/Wii versions, however.
Why does Galactus vow revenge against the heroes in the ending despite not normally caring about human concerns? Well, they stole a device that (in this continuity) allows him to devour planets and he's mad because he has no way to sustain himself now!
In the Wii/PS2 versions, why are Thor and Daredevil locked to the Pro and Anti registration sides? Well, Thor is supposed to represent Ragnarök, the clone of Thor and Daredevil, because at the time in the comics, Iron Fist was disguised as Daredevil as part of a plan to get everyone to think Daredevil and Matt Murdock were two separate people. Note that Iron Fist himself is entirely absent from the roster in those versions, so it's possible that the Daredevil there actually is a disguised Iron Fist.
