Old thread but interesting question. I've love to see more synergy between non-magma or storm colors - more synergistic things beside a few gimmicky multi-color creatures to give players solid reasons to play Blue/Red, Blue/Green, Red/Yellow, and Yellow/Green.
I'd also like to see some of the themes expanded a little more. It didn't really take that many cards to make a goblin deck possible, so adding even a few more cards of a type like undead could create more possibilities for viable themed decks.
New idols could be made that support existing game mechanics, such as an idol that increases % chance abilities, or one that increases the attack power (or Max HP) of all creatures by (X - their cost), buffing cheap creatures.
A little more support for lesser-used deck types like lap decks would be nice, either via new cards or updated mechanics. Maybe the lap bonus could be increased based on how many laps you are ahead of opponents as well?
A new type of creature ability could be added which "activates" when you pay its cost, causing it to fire off the next time a target of the appropriate type (you or an opponent) passes through its space. Harmful ones could be used as land mines, applying debuffs like slow, turning enemies around, silencing them, etc., or they could be used as buff stations for you.
Not sure how I feel about it, but some creatures could have abilities that affect their entire row (all spaces extending from it up to a corner). These would be better on some maps than others, but might still work.
Also, possibly have some creatures that have synergy with a particular item type, like a swordsman who gains extra attack power from weapons, or an armored golem that gains extra HP from armor. I guess this would be something like weapon and armor versions of scroll critical hit. Item-counter abilities might be fun as well, such as an ability that causes a creature to gain bonus attack equal to any HP provided by Armor items used by the opponent, or bonus Life based on attack they gain from weapons.
Note: I haven't kept up with non-US releases, so apologies if the DS or 3DS games added any of the above.