I would definitely want the modern pairings to be kept with their games. Splitting them off adds too many questions, especially since it's pretty popular to ship the modern character with the historical character of that game. There's only a few pairings that would affect anyways (and only really in the Desmond era games) so splitting it out would probably make more issues than it solves.
I think crossovers should go into Crossover Fandom. If you look at the current tagset, most of Crossover Fandom is currently Final Fantasy/Final Fantasy. It wouldn't seem fair to give AC a special crossover fandom when crossovers for other games of the same series are in Crossover Fandom.
Re: Assassin's Creed
I would definitely want the modern pairings to be kept with their games. Splitting them off adds too many questions, especially since it's pretty popular to ship the modern character with the historical character of that game. There's only a few pairings that would affect anyways (and only really in the Desmond era games) so splitting it out would probably make more issues than it solves.
I think crossovers should go into Crossover Fandom. If you look at the current tagset, most of Crossover Fandom is currently Final Fantasy/Final Fantasy. It wouldn't seem fair to give AC a special crossover fandom when crossovers for other games of the same series are in Crossover Fandom.