The following video is an interview with the Creative Director of Beenox, Gerard Lehiany.
Also, this passage from Gamespot explains very well the game's narrative mechanics in greater detail.
"...Edge of Time is not a direct sequel to Shattered Dimensions. The game features an original story that revolves around Spider-Man 2099 and Amazing Spider-Man teaming up to stop a chronal catastrophe that threatens their worlds and just about everything in between. The time shenanigans kick off in 2099 when an evil scientist travels back in time to change the timeline to something a little more conducive to the evil scientist lifestyle. Unfortunately, this requires some murder, namely the death of Amazing Spider-Man. While Spider-Man 2099 tries to stop the scientist before he starts, the futuristic wallcrawler just misses him and winds up getting caught in a time bubble that protects him from the timeline changes that happen around him. The good news is that he retains his memories of how things should be and is able to contact Amazing Spider-Man before his death. The bad news is that the two don't get along, which gets the cross-time team off to a rough start. Will the pair find a way to get along and save the day? Probably, but from the look of things, it's not going to be easy.
The story's time travel angle is more than just a narrative device and figures prominently in Edge of Time's gameplay. The core gameplay should be familiar to Spider-fans who've played previous Spider-Man games, especially Shattered Dimensions. The webslingers will have unique abilities that differentiate them from each other. Amazing is the speedy, acrobatic fighter of the pair and incorporates web constructs into his combat moves of punches, kicks, and leaps. For Edge of Time, Beenox has buffed him out with a new evasion move that will let him dodge just about anything when used properly. Well, almost anything, considering he isn't going to be able to dodge his impending death without some help. 2099 is more of a powerhouse, throwing hard-hitting punches and kicks with a wide reach. His moves have been enhanced with a new decoy ability that lets him create a duplicate of himself to throw off enemies."
Spider-Man: Edge of Time is to be released later this fall. Get ready true believers! Follow the jump to read the full article that has even more info.