This post was originally supposed to be about breaking away from the canon of an established setting. It ended up being about Theme and why Theme is important. It's a bit disorganized, but theme is a weird topic for me. Hopefully you'll still find it worth pondering.
Remember The Theme
Regardless of whether or not you are breaking away from the factual association with the canon keep in mind that the game and setting you are playing, and that your group agreed to play, probably came with some core themes in mind. For example, a Star Wars game should have a focus on adventure and even if there are dark aspects to the universe, you generally don't want the game to get too dark. Star Trek should have a feeling of exploration, negotiation, and violence as a last resort. Super Hero stories should focus on the idea of a person being able to make a difference. Halo should have some focus on hope.
These are simple, but core, themes that ride at the heart of those games. In a real way these are the "feel" part of the game and if a player agreed to play one of the settings odds are they wanted that feel to be there. Otherwise the game description, or desire, gets wrapped up in other things - i.e. a "kick ass type super hero game" has a different feel than a "dc super heroes game."
The point? Even if you are changing canon and venturing into your own version of the world, try to keep the theme there. Otherwise folks will feel left out.
But I Want To Change The Theme...
This could be part of how you want to break from canon, by changing the theme. This will definitely change the feel of the game and get things going in different directions. However, I'd recommend you do it slowly. The feel of a universe shouldn't change overnight. If it does, there should have been something traumatic to make it happen. You also want to make sure your group is cool with changing the theme. Breaking away from the canon story of Star Wars is one thing, making it a brutal and dark universe that focuses on all the horrible things that happen is another very different thing.
But Why Is Theme So Important?
I said above that theme governs the feel of a universe, but how does it do that? Well, for one thing a theme is part of the underlying message of the story. Jedi stories in Star Wars are more than just good versus evil, they're about giving in to emotions and the difference between the fast way and the more thorough way. The Dark Side isn't stronger than the Light Side, but it is faster, more direct, and a lot more brutal in how it does things. Stories about Jedi, the well told ones, remind us that as tempting as it may be to go as directly as possible that there are consequences to that action and you might want to go another way. The theme is still true in well told stories about Sith, but there you have the message of the things that can be accomplished with passion and the desire to achieve one's goals. Neither of these things are necessarily right or wrong - even if most portrayals due to other aspects of Star Wars make it good versus evil - but it is part of a theme. The theme of a Jedi/Sith story is almost always Discipline vs. Passion.
That may be a bit too artsy fartsy though so lets look at the other themes in Star Wars. Good vs. Evil. Simply put the story is that there is evil out there, but that there is also good. They fight, and if the heroes persevere than good can win and things can end up fair and just. It is a simpler view, but one that reminds us that there are things worth fighting for and people who are willing to fight for them.
Star Trek on the other hand as a theme - at least in the shows - that might does not make right. This is why violence is supposed to be the last answer. In essence it gives us the chance, and the challenges, to see that there are other, better ways, and that there are people out there for them.
So what themes are running through your game? What stories and messages are they showing to the players or are your players showing to you through them? Is it even something you considered?