We know that Cap, Iron Man, Thor, Fantastic Four, Incredible Hulk, Uncanny X-Men, Avengers, and New Avengers are all being cancelled and relaunched in some fashion or other. Of those Fantastic Four is the only book at $2.99 pre-Now, and I'd agree that chances are it will be moved to $3.99. But that's only one book out of 8 so far.
You could still be right that most of their books will be $3.99 after this is done. Right now, I think that $2.99/$3.99 ratio is roughly 50/50, not counting Icon books (the creators set the prices of those books, not Marvel). Let's see how it pans out when the November and December solicits come in.