well, I'm gonna be honest with you.... after my single mastery hardcore run, that might just be it for me. but if my opinion still holds any weight, include both but edit Atlantis skills. many skills there have absurd energy costs and some are just badly designed. then make a quest reward in Atlantis that will make it worth completing - like a stat reset if it's possible. once per difficulty.
then ragnarok - the legendary craftsmanship still feels wrong. your item can actually get worse after the upgrade. maybe the values don't get changed and instead of random affixes, make the item socketable instead. again if it's possible
edit: wands or thrown weapons. if it's just one or the other, can't you make it like some are throwing weapons but have the attributes of a wand but projectiles of a staff? i mean different staves have different projectiles (the MI staff with a pierce damage, staff of the cosmos?, carnyx) so maybe it's possible with throwing weaps