Something about Mage Tower really appeals to me, even moreso now that the Tom Vasel preview confirmed much that I had hoped about the gameplay.
Without having played the game myself, it's probably a bit premature to start posting variants, but what the hell! I'll keep it in the General forum rather than Variants, as a token gesture towards conventional manners.
In the normal game, players draft eight cards at the beginning of the game, which makes for a broad variety of possible strategies. The (potential) issue I have with this is that players can end up building a deck that is fundamentally weak against one or more of their opponents, and it becomes obvious that they are going to lose within a few turns. On the scale of adaptation that runs from MtG to Dominion, Mage Tower is closer to the MtG end than I (think) I want it to be.
My proposal is that cards are not all drafted at the beginning of the game, but instead the draft happens several times through the game.
* Before the game begins, players draft five cards clockwise, keeping four.
* When a player exhausts his deck, there is a new draft phase, drafting another five cards in the opposite direction to the previous draft. Then all players shuffle their discard piles and place them beneath their draw deck.
* I would also move the draw phase to the end of the turn instead of the beginning, because that's always an easy way to cut down the start-of-turn AP, and rule that a draw during the turn (ie from a card effect) does not trigger a draft - the draw is wasted if the deck is empty, and the draft happens at the end of the turn instead.
As I said, I don't have any play experience to know whether this would work, or even whether the normal rules are so awesome that this variant is pointless. But I'm quite excited by what looks like a genuinely unique game (I think even the designer would admit that the graphic design is a bit lacking, but it seems like the game itself will be sufficiently fun to eclipse that weakness), and cannot help wanted to poke at its rules!
I brought similar issues up with Brimmer, the game's designer. He feels that the game is solid as is and experience playing it will confirm that. However, he is open to changing things up in future expansions.
My own suggestion was to have a prize card similar to the Kickstarter promo "Ennoblement" (which is a draft deck single, not a prize card) that would provide access to the draft deck in game, not just at setup.
Another idea is to have an always available "Market" made of the top 6 cards of the Draft deck. You can buy a card by paying gold equal to its Energy cost. When a card is bought, it is immediately played by the purchaser, and a new card is added to the Market.