You can trap Eternity-like beings into the Eye as well as indirectly manipulating the soul. The Eye is all Seeing while the Soul Gem isn't. Eye give 1st person view, 3rd person view and bird's eye view with everything happening in the multiverse in every realm in every dimension.
The Soul Gem alone can not effect Eternity. Though it has a more direct effect on a soul, it usually sends that soul to the Soul World for manipulation. The Soul Gem does not see all things happening simutaneously throughout every dimension in the multiverse.