Personally, I play PvP mostly. You can get more score and money, and it's more interesting - you don't get the same decks over and over again.
As for upgrades, I haven't got past the false gods quest yet, mainly due to people with low scores fielding decks that are totally unimagivative grind decks (Phase dragons, etc) and it's against these that I lose score. People that I beat are people with high scores, and new/slightly imaginative decks (ie, non-grind), but I'll probably play PvP for money, then grind the gods.