If need be I can make a laundry list of games that have a tutorial or training session that do not cover everything in the manual. I read the manuals and I find that there is always something that the game neglects to mention. This has usually been the way a function of the game works. The game will say touch B to do X, but then the manual will say touch B in this situation to do X, press B in another situation to do Y, etc. Otherwise there is some story or background stated in the manual that does not make it into the game. Manuals sometimes have character descriptions, back stories, or environmental information that will mention something the game will take for granted. For example a character back story in a manual will say something to the effect of "The elves homeland is X." Then in the game it will say something stupid like "Take the elf character home." And you can select from town X, Y, or Z.
I will admit that printed manuals may be useless, an electronic manual is just as effective. Final Fantasy XIII has done a good job with an in game electronic manual. Oh, and if anyone has ever said RTFM for anything and is now advocating removing manuals for games, STFU.