I personally would love to see them adapt the Spiderman Unlimited story line to the main comics. Have High Evolutionary obtain some sort of advance tech that enables him to create a copy of Earth and for it to have been a secret project he's been working on for untold years. Besides I'd love to see Sir Ram and Tiger to become canon characters. Tiger especially because I think a comic book take on him would be good to see since he valued honor and I can see Peter having an interesting dynamic with him. Though I don't know if a Carnage and Venom team up would work as Venom is a hero now, but I can see how the synoptic could fit into comic lore perhaps as a sort of symbiote hive that gets disturbed by beastial construction workers and sends out a sort of signal that drives Venom and Carnage to Counter Earth. Carnage I can see being motivated by the desire to witness the coming destruction caused by the Synoptic and Venom I can see being driven by a desire to protect the future of his species. I remember Venom saying once in a comic that the symbiotes don't care about their offspring but do care about the survival of their species so if the Synoptic was tied to that I can see them both instinctively being drawn to it.
Also I'm curious as to how Peter would interact with Naoko, Shane, and Counter Goblin especially since it was pretty obvious in the cartoon that Goblin was Shane's dad and didn't like Peter stepping in on his turf.