I was hoping that Takamaru would be playable in Super Smash Bros 4, but I am glad that Sakurai made him an assist trophy.
He still has the potential to be a playable character, since he would be the only character in the roster that uses a sword in a Japanese style. His game mechanics from Murasame Castle could be transferred over to Smash Bros (His sword reflects projectiles except for fireballs, throws different types of shurikens, and Inazuma Lightening as his Final Smash).
However given that the roster now has 7 sword-wielding characters (Mii Fighter counts too), they are taking up around 1/5th of the current roster of 36 characters. 1/5th is a huge chunk of the roster, and adding Takamaru would make the roster feel uneven in my opinion. I am sure there are other reasons why Sakurai would not want to make him be playable, but I am not entirely sure. Probably some game mechanic or technical issues, etc.
One day, maybe he would be promoted from assist trophy to playable character in Super Smash Bros 5 just like Little Mac.