I used to think that giving everyone a projectile was a bit silly (mostly characters like Sonya who seriously don't need it), but all things considered, it's one of the main things that makes MK stand out from other 2D fighters. Much like the block button, it's not going anywhere.
Though anyone who claims that all MK characters are 'basically the same' clearly hasn't played it for very long. The characters have just as much variance in play styles as characters in Street Fighter do - the only real difference in that regard is that MK is generally slanted more towards offense whilst Street Fighter is slanted towards defense. Just because there are many tools that everyone has one of (such as projectiles) doesn't mean they're used in the same or even similar ways.
I personally think that NRS are onto a winner with the track they were going down with MK9. Obviously the balance needs fixing, but the core engine is pretty damn solid. Not to mention that it's one of the only fighting games other than Tekken that uses a 'one button per limb' system (seriously, why don't more fighting games use that? It's genius!)
There are only a few changes I'd like to see to the basic character/game design:
* Get rid of stance switch. Seriously, it's pointless.
* Unique air normals a la Injustice
* More ground strings (ideally double the number in MK9, though I appreciate that that's rather a tall order...)
* Change. The. Damn. Meter System. Gaining zero meter from actually hitting with attacks, yet tons from having them blocked, is ridiculous. Significantly decrease meter gained from blocked attacks, and correspondingly increase the amount of meter gained from attacks that connect.
* Maybe tone down block damage slightly. Don't get me wrong, I love the block damage in MK, but it gets a bit excessive at times. A string that does, say, 9% damage if connected, should maybe do 2.5% on block, not 4% as currently.
With respect to characters having different amounts of health... that could certainly be interesting, so long as it's not too extreme. Sheeva having, for example, 10% more health than average, and Cyrax and Kabal having 10% less, would work pretty well. But no bigger leeway than 10%.