Chaos Jackal said:
I don't think any 3DS games come with paper manual. The manual is digital, you can select the option when you pick the game on the starting screen.
Many games have and still do include paper manuals, but are slowly moving away from it (possibly to save paper). For example, XY included a 6 page foldout manual, and 1 page of that was a cover, and 3 pages were warranties, copyrights, and warnings, leaving just 2 pages to briefly explain the Player Search System and the controls.
Compare this to Black 2 (the most recent predecessor), which included a 24 page booklet manual, which went into much greater detail on the various features of the game, From basic controls, to Unova Link, to the C-Gear, and even Pokemon Global Link. Clearly we're seeing a movement away from paper and to digital.
I'm only a little sad for this, because there are those occasions where you would like to look at the manual and play the game at the same time (preform the instructions while reading them, perhaps), but these were relatively rare. If I ever looked at a game's manual at all in the past, it was about some obscure feature or detail, which digital manuals serve just as well for, if not better.
