Sakurai has addressed the absence of the Ice Climbers in a Famitsu column, and it's due to the 3DS's hardware limitations as suspected. He cut them from the Wii U version as well because he wanted both versions to maintain the same roster, even though he did get the IC's working in the Wii U version.
In the same column he also addressed the different release dates for the 3DS and Wii U versions, and it was due to both games needing separate debug periods. If both games were to have the same debug periods in order to release them simultaneously, it would take so long that the games wouldn't be able to be released until 2015.
Source: http://nintendoeverything.com/sakurai-addresses-ice-climbers-absence-in-smash-bros-wii-u3ds-and-more-in-new-famitsu-column/
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