Lucas and Wolf: Came under too much fire for being "Clone" characters despite their Luigification.

Squirtle and Ivysaur: Greninja stole the slot as the Water Type Pokemon, and Ivysaur was caught in the crossfire.

Ice Climbers: The Pathing AI used by Nana was unable to work on the 3DS due to Hardware Limitations. Had the "New 3DS" been the original model of 3DS, it would have worked. If you complain that "Rosalina and Luma use the same thing", you fail to understand the simplicity of Luma's code compared to Nana's complex one.

Snake: Politics. Nintendo and Konami don't exactly get along that well anymore. And no reason to bring him back because Metal Gear Solid 5 did not come to the Wii U.