In a column in Famitsu (found by Esuteru), Masahiro Sakurai revealed that the reason for not including Ice Climbers in Super Smash Bros. for 3DS was the handheld's lack of power. There are a lot of characters in both games, but some are missing. An additional reason for the absence was that Nintendo aren't prioritising these characters, and they likely won't get a new game in future.
Sakurai also revealed that the two different release dates made it possible to launch both games this year. By trying to release both games together, their different content, plus the time it would have taken to put them both through QA, meant they would have collided and both may have had to have been released in 2015. Luckily this isn't the case.