Honestly, I think a tiny part of my mind thought this would happen (at least him not being in, the Assist Trophy thing still sucks) for one reason: Hyrule Warriors.
When Hyrule Warriors was released, Skull Kid wasn't in it. There was an outcry, and then he became DLC. Seems like prime support for Skull Kid.... except Hyrule Warriors came out after 2015, when the cut-off-date was for the Smash roster, which I hadn't realized until recently. Once I did I got a little bit cautious, because if they didn't see enough support for him to be included initially in HW, then them considering putting him in base might not be too likely.
Unfortunately that turned out to be right, and with him still being an Assist Trophy we might not have hope for DLC. But... maybe we do? Nintendo listened and eventually put Skull Kid in Hyrule Warriors as DLC. If they haven't already decided on the DLC characters (and since they aren't coming out for a year they've got time), maybe there's a chance we could get Skull Kid in as DLC, even if he is an Assist Trophy.