I think all the characters were worked very hard on. In fighting games it's extremely hard to balance characters unless you have like 2 characters. If the competitive crowd was bigger (In comparison to the causal audience) perhaps Ike would of gotten more attention in regards to that environment but like all game companies their main focus is on making money (so they target the bigger audience).
I can understand you feelings though.
I generally agree with Kirby Knight here. I think that the game designers wanted to make every character unique and at least playable this time around. They definitely succeeded in giving each character the right "feel." Sonic feels like he's lightning fast, Ganondorf and Bowser feel like they hit like a truck, and Sheik's combos make you feel like you're a Ninja.
I also believe that special attention was given to Snake, seeing as he was the first 3rd party character, and they made sure to go out of their way to make him stand out. This might have actually affected his balance with the other characters to an extent.
The last thing that the designers wanted to do was to let down a franchise's fan-base because their character sux. Everyone wants their favorite character from their favorite franchise to be equal to the rest of the cast, but this is simply not a perfect game, and it is simply not a perfect world.