Do you use exFAT or FAT32? Try booting on a FAT32 SD-card. I once made an update with Atmosphere running and exFAT driver stopped working, so I had to reformat my SD to FAT32.
But first try booting clean atmosphere without additional modules.
Do you have your emuMMC configured correctly? Check emuMMC manager in Hekate.
I would worry if your SysNAND has some nsp installed and you went online with that. This could lead to console ban.
I use Atmosphere for now, because in the current state is has more features implemented that I'm interested in.
LayeredFS
Signature patches
Homebrew launcher
Modular boot config with hekate
Doesn't crash and is pretty stable.
I wanted to use ReiNX at first, but LayeredFS isn't working there...