The only reason I could see someone saying "Make it a different game!" is the fact certain cards/themes would not fit within the current affiliations, but I do not see anything to prevent them from increasing the number of affiliations.
Or because it is ridiculous to feel the need to add more stuff already where the game is so new, or because it will just make it even harder to support each faction, or because it would also make sense theme and timeline wise to have a second game and thus prevent all of the flaming and hate mail that would arise from having Darth Maul and Darth Vader fighting on the same against little Anakin and Luke Skywalker. And because it would allow them to have another game, thus another product and more sales. And because as I said earlier they have a game for the Hobbit and a game for Lord of the Rings that are separate from each other as well as Hobbit expansion for LotR LCG.
I think FFG is smart enough to avoid the mistakes of previous license holders like WotC and their ridiculous mish mash of every faction and character ever seen in the SW universe in to one miniature game.
Also consider that FFG tends to have a fixed limit of factions in their other LCGs like AGoT, their biggest by far, has 6 factions and will never have more. Cthulhu is the only one that got a faction added to the game and I cannot speak to how successfully or unsuccessfully that went. I really don't see the need for more factions in this game beyond what we already have. Lots of design space already there.
To be fair, neither Decipher nor Wizards built affiliations into their respective card games as a fixed mechanic, let alone one that is so central to the game's gameplay as this is. It was therefore easier to introduce multi-era elements into them, continuity issues aside. Since FFG decided to go with their tried-and-true method of dividing cards into several factions, it would be very difficult for them to expand this game beyond the Classic era without each affiliation's playability becoming a balancing act. Unless they figure out a way to write themselves out of this corner, Star Wars: The Card Game should be considered a game specific to the Classic era.
Regardless of my feelings about the other publishing eras, both positive and negative, I would prefer that they stick to the Classic era for as long as it proves feasible, especially with Episode VII being slated for 2015. Assuming that film gets a May release, as all previous films in the saga have, that gives us time to see just under five Force Pack cycles. I think there's easily enough material to pull from the Classic era to cover that amount of content. I'm just hoping that new film leaves enough of the Expanded Universe intact to provide additional avenues for this game to explore. A lot of fans were turned off by the prequels, and the pressure is on for J.J. Abrams to give us a film that will evoke the feeling of the Original Trilogy, albeit in a different time period. If he succeeds, Star Wars will no longer be about the Original Trilogy vs. the Prequel Trilogy, but will become a series of films telling different chapters of a grand story. And so I think that that is the idea that FFG should proceed from, should they decide to make this game - or any of their games - expand into other eras.
"Truth has power. And if we all gravitate toward similar ideas, maybe we do so because those ideas are true…written deep within us. And when we hear the truth, even if we don't understand it, we feel that truth resonate within us…vibrating with our unconscious wisdom. Perhaps the truth is not learned by us, but rather, the truth is re-called…re-membered…re-cognized…as that which is already inside us." Peter Solomon, The Lost Symbol