1. Reboot The Series
With all my previous points possible to interweave into the ongoing canon, another thing to do would be reboot the franchise altogether. Take the most basic core aspects of what once provided a solid canvass - like twin-protagonists in two timelines, an Animus and a Da Vinci Code-style plot that needs stopping, revolving around the Assassins vs. Templars - and have a fresh start. Right now the story is in tatters, I doubt you could even name any of the pivotal modern day characters outside of Desmond (no, 'Desmond's dad' doesn't count), and it might be the most freeing thing for the multiple studios working on the series, to cast off trying to maintain any sense of continuity with a narrative setup
that's already so far gone. There could always be cameos or easter eggs towards the likes of Ezio, Altair or Desmond in the grand continuity if Ubi wanted to maintain ties to their original works, but how awesome would it be to take the things that work from the old games, chuck away everything that doesn't, and start again? Honestly, I think the fans would actually embrace that at this point.
Let us know in the comments what you think of all these suggestions, and what your own would be to get Assassin's Creed back on track!