One thing I really love about Mortal Kombat X is that NetherRealm really listened to lots of what people wanted in the game, and added things in to appeal to all types of their audience.
Remember, the average player of the game is not a pro-tourney player, so they included stuff for casuals as well.
One of the casual things is the Faction system. That way casuals can feel like they're contributing to something, completionists can collect more stuff, you can get easy Fatalities (Faction Kills) that are simple to pull off, etc.
Could the Faction system be more hardcore? Yes, but I believe in a Kombat Kast NetherRealm said it was designed with casuals in mind.
Having said that, are there improvements that could be done with the Faction Wars? Absolutely.