I'd do Desmond-Era (AC1, Ezio's stuff, AC3, Black Flag, Freedom Cry, Liberation, Rogue), Unity, Syndicate, Origins, Odyssey. There's a cohesion to the games pre-Unity, and while Shaun and Rebecca do briefly briefly appear in Syndicate, anything requesting Desmond in that era could still go in Desmond-Era while mentioning wanting the later timeline.

There's a chunk of fans who've only played Origins and Odyssey who won't really request outside that, so they should have their own little boxes. There's a cohesion to the stories before the next-gen plot retconning and reshuffling mess re: Juno that were the games post-Syndicate, but Unity and Syndicate should be separate to encourage separate nominations rather than grouping them where they'd be overshadowed by Origins and Odyssey or the Desmond games.