Honestly, I've been in Mega Man 9 mode in such a huge way that I kind of forgot this game was coming out. The above image, which you can click to enlarge, and the following info come from the latest Coro Coro magazine.
The two versions of the game will primarily differ in the variety of cards they offer, the variety of Noise Changes they offer, and the Finalized Noise forms. Not much of a surprise considering the way the previous titles are treated.
The game will feature ten "terror" Noise Changes, which are likely to be darker versions of the initial Noise Changes, i.e. Ox, Cygnus, Harp, etc, although this is not explicitly stated. Not much has been released info-wise, but seemingly Rockman's type (I'm guessing elemental attribute) will be random when using one of these forms. These forms will be introduced later on in the progression of the story.
In other little bits of info, when you delete an enemy with 100% or greater noise, you'll receive a random card as your prize. High noise levels also invalidate an opponent's invisibility status. Sounds a little strange.
Finally, Capcom will be releasing "noise modification gear," which are cards seemingly similar to the command cards in MMSF2. There are three varieties: Noise Cards, which increase your abilities and up to five types cards can be combined, Reson Cards, which strengthen your finalized form, and allow you to share these benefits with friends you've assembled in your "team," and White Cards, which just allows you to add more White Cards than you could get in the game yourself.
News Credit: COCOROG