Personally, I'd favor stall decks. However, I'd make them harder to play. Instead of cards like lightning bolt and firebolt and shockwave being the strongest ones, I'd narf direct damage spells, and buff abilities like ghost of the past and scorpion. I'd add in more hand/deck defect abilities, like milling. I'd replace firebolt and shockwave with field effect spells, like flooding, and make the strongest form of control AoE spells. That way, the most powerful deck can prevent you from playing cards, and kill multiple cards at once, gaining card advantage, but you have to be really good at the game to be able to handle it.
Right of the bat, I'd rebalance every single mono deck. Fire rush, graboid rush, and USEM are about how strong I'd make every single mono. I'd make immortals cheaper, but less difficult to kill. (Immortals stunned or frozen lose their immortality). I'd make phase shield easier to break (direct damage destroys them), but I'd give aether an alternate form of damage prevention. (Phase out, your life total cannot change until the start of your next turn). I'd give air a card called "take flight", which lobotomizes and doubles the attack power of a creature with flying. Darkness' gargoyle + devourer deck is about as strong as it should be. It'd rebalance death so it ramps better. Vultures would gain +2|+1 each death, making the virus + vulture a more feasible mono. I'd make chaos seed and chaos power two separate cards. I'd give gravity more damage spells, and more field control. Cards like "Gravity warp", enemies cards are randomly pulled toward this point, and "Zero G," creatures attack power in this area are halved. I'd give life a treant card. All spells now target it, and it has a formidable amount of health. I'd get rid of sanctuary's overtime healing, I'd make holy flash cloak your field and precog their hand, and I'd get rid of luciferin's healing while rebuffing the nymph's attack, but I'd make angels able to target the player. I'd limit miracles to one per deck. I'd give time the spell "fate change, destroy the top card of your opponent's deck". I'd give water more field control.
Hopefully, with all the mono's re-balanced, people will find duos strong enough to beat false gods. Gravity+water control would be amazingly good, maybe the best deck in the game, but it'd be easily counter-able by field protection from things like cloak and the new holy flash. Light, instead of being the element of healing, would be the element of field protection. Straight creature spam decks would fail miserably, unless they came with cards like Phoenix that are stronger versus control, or intended to dominate.
I'd get rid of quantum pillar. Unupgraded nova would do the same thing it currently does, but for one. Upgraded it would be the current unupped nova. Rainbow rushes would be fast, and possible, but destroyed by control.
I would probably ruin the game =P
