I've never even noticed that, let alone had any problem because of it. I have always been flicking my smash stick for aerials, and I don't see why anyone would ever hold it after using an aerial anyway. Still, that is a rather bizarre change.
The one time I held directions with it in this game is when I was messing around with the new smash stick charging mechanic. Can't see myself using it, the A button works just fine for my smash attacks. The only exception I'd make with Ike for using the smash stick is for a quick d-smash since I sometimes get a slight but crucial charge when I input it with the A button instead.