Prognosis: Mmm...while Sheperd has a wide array of powers that alone make him an interplanetary threat, I feel Apocalypse's powers outranl him. While Apocalypse may be a bit weaker in other areas and a bit vulnerable in some areas (Sheperd's Matter Manipulation, Chronokinesis, and Electro-magnekinesis) Apocalypsr just outpowers him in many other areas as well as equal in a lot of parts.
I think even having not battled him before Apocalypse could easily adapt in the fight.
Imo Apocalypse takes this one.