What if which cards you added to your arena deck costed points? Naturally they would need to add more points and increase the cost of arena abilities, but I think it would be cool. Your Oracle cards would be free but say like a pillar could be 5 points and a Dragon could be 20 or something like that.
I was also thinking that maybe card costs could fluctuate based on usage. Like Supernova could cost 40 points because everyone always uses it but Graviton Mercenary only 10 because no one uses it. You can build a Ghostmare if you like, but you'll be shafted for points and may have to give up double draw if you want to afford the whole deck.
The only problems I see here are the obvious one of needing a lot of work coding and balancing values, and that big decks would be hurt (but seriously who makes 35+ card arena decks?)