The reason for splitting Zelda/Sheik and Samus/Zero Suit Samus into separate character slots? 3DS wasn't up to it.
Super Smash Bros. director Masahiro Sakurai revealed in a recent interview with Famitsu that limitations in the capabilities of the 3DS hardware prevented the inclusion of characters who transform into alter egos with completely different appearances and move sets.
That's why Zelda and Sheik now occupy two discrete character slots in the 3DS and Wii U Smash Bros. games, and the same holds true for Samus and Zero Suit Samus. In previous series entries players using these fighters could switch from one form to the other mid-match, and Sakurai was asked to explain the reason for the change.
"It’s basically due to the 3DS’s limitations,” he responded. "“It was impossible to have both characters exist together [as one] on 3DS." Sakurai seemed to think, however, that the change might be for the best, as he postulated that "reaching that limit can sometimes lead in good directions. Transforming characters had the drawback of ambiguous tactics and such, and I believe that they have become more fresh now."
This isn't the first time we've heard that the 3DS's relative lack of power has affected the series' newest entries. For instance, it was revealed not so long ago that Ice Climbers, veterans of the last two Smash entries, were cut from the roster of the new titles because the development team couldn't get them running properly on the handheld. Another recent Sakurai quote revealed that the Circle Pad Pro doesn't work with the game because it is already pushing the portable system to its limits.