My thought for a multi game campaign would be to copy the campaign system from Imperial Assault. This would result in more than 2 players needing to play as teams, but I think it would be relatively easy to implement.
If you aren’t familiar with IA, it’s basically a GMed dungeon crawl, one player plays the Imperials, all the others play a party of rebel heroes who work through a branching tree campaign ala a choose your own adventure story, but the choices are made by winning or loosing missions. At any given time the rebels will have a story mission to do and possibly a few side quests as options. The imperial player may also be able add missions to the players mission deck, and if they choose not to do that mission next, the Imp player gets a bonus for future games.
The key is that, while all this governs what mission the players engage in next, the missions themselves are basically stand alone games. There are mechanics in place to scale the imperials power level up as the heroes gain better equipment and level up, so the campaign system doesn’t need to worry about that so much, it happens automatically within the rules. This means that the actual missions could be resolved in other ways than playing IA. Some missions could be an x-wing game, some a legion game, some an Armada game, and so on. You write a branching story line that includes scenarios using the different games and they fold in naturally.
What would need to be done is to create a set of heroes each of which has at least some skills and upgrades that are applicable to each game in the campaign, and the create gear and rewards that that also effect each game.
So, perhaps, the rebels raid a fighter base as a legion battle. If they succeed, they have stolen some fighters and can upgrade their z-95s to x-wings in future x-wing games. A successful x-wing battle to rescue an escape pod means a bothan spy got out with data about the exact location of the empires new battle station, leading to an Armada, legion, and x-wing trilogy of scenarios, each of which have to be won for the rebels to win the campaign. Wait, that sounds familiar....