In a Reddit AMA, Assassin’s Creed IV: Black Flag Lead Writer Darkby McDevitt said that it is unlikely that Connor from Assassin’s Creed 3 will return in future games. he also ruled out that one of the games will take place during modern times.
He said that while the team loved working on Embers – an animated short going back to visit Ezio outside of the games – that team is now working on other projects. So it’s not likely that Connor’s story will continue in either a video or video game.
As for the modern day setting, he stated:
“I doubt we would do a modern day AC. There are just too many mechanics we would have to develop to make it [believable]…vehicles, plausible modern cities, a hue array of ranged weapons, etc.”
“The modern day will most likely remain as a ‘context’ for all future games, something o tie them all together. Watch_Dogs will scratch the itch for a modern day AC. Just wait!”
McDevitt also went on to say that it is also unlikely that Ubisoft will resolve the Assassin/Templar conflict. “As for the Assassin’s Templar storyline resolving. I don’t think so. [It's] been going for 80,000 years already. Why stop it now?” After all the conflict isn’t just based on two organizations, but two competing philosophies that we still haven’t resolved to this day.