Yes I mean OCS/AGA native stuff. Games & demos, the stuff which (IMHO) the Amiga is all about. Take away that and all you have is a damn slow Linux-esque computer with an Amiga keyboard.
3.9 boot speed is fine if you have the latest 3.9 EPROM or a flash device (Algor, Kickflash, eFlash, Deneb etc) so you do not need to reboot during POR.