Natural disasters sound tricky. First you’ll need an explanation, something happened before Day 1 that triggered enough natural disasters to be relevant in-game. They’re not exactly a common event IRL. If you get caught in one you also shouldn’t have any reasonable chance of survival if you’re unprepared, so preparation will be key, either by getting out of the way or riding it out. According to the wiki, the radio will eventually pick up signals from other factions. The radio could also serve to warn players of incoming disasters, and then they can prepare. I like this idea.
Kevin Granade’s Design Outline states that supernatural factors have to be a) fun and b) have a Cata twist. That goes for the horsemen, demons, angels, mythical creatures, non-Euclidian stuff, and Ragnorok (1 apocalypse isn’t good enough for you?). Horsemen would probably only exist as a mod boss. Demons might be associated with the unfinished hellmouths. Angels, let’s not give the survivor’s too much hope. They certainly can’t be associated with God or heaven, and they’re not on the survivors’ side. Mythical creatures sounds iffy. I can’t think of a good reason for them to be present, and besides that we already have wolf people. THE Ragnarok doesn’t sound like a good idea, considering that involves a great, climactic battle (the player will likely never be on that level), natural disasters (already discussed), and the flooding of the world (a bit much for a game restricted to the New England area). The Biblical equivalent involves the Horsemen of the apocalypse, and honestly I don’t see it as being something the player should be able to deal with, either by fighting or running.
Radioactive wasteland might be a cool world generation option, either the US or some other government bombed the country to hell and back as a last resort. Radiation everywhere. Most houses flattened, forests scorched, supplies scarce. I know there’s a world generation option that lets you select between normal world generation and a “desert” world, although I’ve never touched it.
Superpowered NPCs - only achievable through extensive use of CBMs and maybe mutation. You might see heavily mutated/modified NPCs as the game advances. NPCs with CBMs might need some specific balancing so that the player doesn’t get assassinated with invisibility or Time Dilation.
Areas that have been screwed up by time travel would certainly be interesting (knights vs. dinosaurs, oh yeah). Considering it’s already canon that scientists messed up pretty badly with interdimensional travel it’s not too farfetched that they would have been experimenting with a dimension we already knew existed as well.
An invasion doesn’t sound plausible, keep in mind that before the Cataclysm according to lore the United States was in full “USA! USA! USA!” mode and presumably had even more firepower than ever before, both among civilians and in the military. The military and 99% of the country was overwhelmed regardless, so I can’t imagine other countries’ ground forces successfully penetrating zombified America.