Merging X&Y Version with Main Video Game Series would be my preference as someone who nominates for Pokemon in exchanges. While X&Y is a distinct subunit of the main series, all of the main series games are set in the same world and characters from one game can sometimes be met in another, with the same characterization and personality. Additionally, as someone who nominates ships for characters whose main appearance is in different games, having to make a crossover for characters who canonically exist in the same universe is counterintuitive.