The upgraded version and the standard version are meant to have 2 different types of synergies. The standard has synergies with the card drawing of
Time and the upgraded has synergies with the card denial of
(Reverse Time, Eternity).
I really want the upgraded version to have a harder time using its skill but better stats and stronger overall. There should always be a reason to keep the standard versions of a card in the game and if the skill on the standard Prophet seems better, I've done something right. If the design of the card is right, which it may not be at this point, you should want the standard version in some cases and the upgraded in others but the upgraded should be the superior card in the end.