The most important part of the game is making them feel immersed. Arkham Horror is popular because it captures the feel of the Mythos.
Star Wars is about good vs evil, Jedi vs Sith, the Rebellion vs the Empire. This means there must be 2 sides, as shown in pretty much every game made about star wars. Either the game is co-op vs the empire, or it is competitive with 2 different sides as shown with the original TCG, the LCG, Imperial Assault, X-Wing, Armada, Legions, and Destiny. You can't have a co-op game of Star Wars where Luke Skywalker teams up with Vader to defeat an Imperial Officer.
Now you could theoretically have 2 separate scenarios, but that is basically 2 separate games in one, which is inefficient and makes no sense. You could have both factions face the same scenarios, but that means the scenarios have to work for both sides, which seriously limits design space. You can't have Vader fight Vader. You could create scenarios that you modify, but that still is limitting and basically means each scenario is 50% or larger than in other co-ops to allow for different sides.
People don't want to be random Bounty Hunters, most of whom worked for the Empire against the Rebellion, they want to be iconic characters from the story. There is a reason FFG uses named characters common to all their games, it creates familiarity and investment. It's why you don't play as random Gondorian Spearman in LotR.
The game has limits in resources, and in what they can do. Making both factions playable makes no sense, and would make the game unworkable.
The best option is to make it Rebel only, and the Empire is the scenarios.