I have the same issue. I have a MacBook Pro (Retina, 13-inch, Early 2015).
If I shutdown my computer or the battery dies, when booting up the whole USB bus is turned off. No keyboard or trackpad. It also takes a long time to get to the login screen.
The only way I can get the computer to see the USB bus again is to remove everything plugged into the computer, do a SMC reset, then a P-Ram reset.
I think my issues is that I have one of those Transcend JetDrive Storage Expansion Cards in the SDXC card slot. I don't think the mac likes having that plugged in at start up. But that should not be an issue. Going to take my computer to an apple store and have them check it out.