Fridge Logic - 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?
It gets better: he fights you first as Venom, and later as Scorpion (together with Green Goblin). So apparently, after being defeated as Venom, he changes back into his old costume for no reason...
I remember a story in Spider-Man where Gargan fought Eddie Brock (who had recently gained new superpowers as "Anti-Venom"). Brock proceeded to severely harm the symbiote, so as a stopgap while he waited for the suit to regenerate, Gargan used his Scorpion Suit.
How about this one from the first game then: okay, the nanites in the heroes' bodies allow them to breathe, see and speak underwater, and roam the kingdom of Atlantis freely. But how come you can pick Human Torch and/or Ghost Rider to play there?
Well, Ghost Rider's flames are not physical, they're hellfire, so they burn independent of air. Human Torch? Okay, you got me on that one.
Reed had made some ridiculous "fire powers work underwater" gizmo a few times before, why not now?
Although the Secret Invasion hadn't happened yet when the first game was made, Spider-Woman can be in your party when you interact with the Skrull Empress.
This one is simple, the Secret Invasion that happens in the game continuity is simply different than the one in the comics.
Or maybe that Empress wasn't Veranke. Hell, maybe this took place before the Illuminati visited the Skrull homeworld.
Game's an another Earth not Sarth 616 so Secret Invasion probably didn't even happen I mean after all Civil war ended differently