Why were the X-Men and Fantastic 4 absent? In the second mission, just before the attack that dragged New York into Chronopolis, Nick Fury sent the avengers on missions around the world, it can be assumed that he also sent out the other super teams, and we can assume that they simply weren't within one of the districts that Kang took for Chronopolis. It can be assumed that the villains they went after were Doom and Magneto
Furthermore some of the villains in that level were implied to know something about Kang, or at least something, it is possible he hired them to cause this chaos to thin out the heroes, so the Avengers weren't at full strength in Chronopolis.
There's the more obvious reason, only part of New York was taken, and neither the Fantastic Four nor the X-Men made it in time to stop Kang from taking it.
Also, in most continuities, the X-Mansion is in upstate New York, not New York City.
Loki in the first game was hellbent on destroying Earth in revenge, while here, he simply takes over Asgard and Egypt and causes trouble for the heroes without attempted genocide, and even works with them at one point. Why the change? Well, it was confirmed that Loki's more monstrous behaviour in "Avengers" was because he was corrupted by the staff Thanos gave him. Loki had this staff in the first game, but not in this one. The staff here just a spear, no Mind Stone to be found.
Assuming Kang's time-reversal in the last level didn't undo it, let's hope Nueva York was evacuated before Kang sent his sword-ship careening into it.
Carnom is already a creepy concept, but consider that the Venom and Carnage aren't just Symbiotes, they're people too. Even setting aside the possible Body Horror that could've occured from it, imagine it like this. Eddie Brock isn't a great guy, he's a supervillain here, but it's a stretch to say even he deserves to be fused, physically and mentally with an Ax-Crazy killer like Cletus Kassidy.
There's a whole timeline run by HYDRA, and the people there are so into it, that the heroes can't do a bloody thing about it besides just trashing their statues and parade. Best not to imagine what Captain America must've thought when he saw all that.
What's worse? The people of HYDRA Empire should count themselves lucky the Mutants aren't in Chronopolis, considering a certain, very powerful and dangerous Mutant is a Holocaust survivor who'd likely have a lot of things to say and do to such a place. Granted, HYDRA is an Asshole Victim in any case.
Some sidequests reveal that while some people got the luxury of having their homes and timelines added to Chronopolis, others like Spider-Ham, Cap-Wolf, Throg, Maestro, and so on didn't even get that. They're stuck in a completely alien world with little to nothing familiar.
