My thoughts on the matter are that Ice Climbers and Chorus Kids were cut extremely late in development (like early 2014 late) and replaced with Dark Pit and Lucina. My opinion is that Doc was always in the roster and was shifted around to not make the other two clones look ridiculous in the CSS, as he's had a lot of work on him compared to Dark Pit and Lucina. You combine that with all the Melee nostalgia nods in the game and Doc makes a lot of sense. He was planned for Brawl, remember.
The smoking gun for me is the new Ice Climbers render/pose and Chorus Boys trophy and the treatment of Rhythm Haven as a playable series with trophy representation and Smash Run.
If we remove Dark Pit and Lucina, we can swap Game and Watch with Doc (and move Game and Watch to be with the other retro characters) and Ice Climbers and Chorus Boys fit cleanly in roughly the same area as Lucina and Dark Pit. Actually, the clone corner itself is located where Chorus Men would have been, since they were released in 2008, after Wii Fit Trainer, but before Shulk. This also might have allowed Shulk to move up a row and leave the third parties + mii to sit nicely at the bottom row.
And I entirely blame technical hurdles. Both characters had unique game play behind them that was just too much for the 3DS to handle with the quality Sakurai demanded. He wouldn't have cut Ice Climbers without a damn good reason to do so.
I think either both will be DLC if they can work out the issues with enough time, or will be exclusive to some re-release of the game on the new 3DS, or Ice Climbers at least will be in Smash 5. Guaranteed.
I guess that's just something we had to expect with a handheld Smash. But as much as I love Ice Climbers and miss them dearly, the handheld version is probably the best thing to happen to the Smash series.