Answer:
It depends upon your play style, really. I own both games and enjoy them. However, the mechanics and game player are completely different between the two. In Innovation, you do not know what cards are available until they are played in front of your opponents. You don't know what they have and it plays more like Civilization than Dominion.
Dominion has a set of cards that are always visible. You know what your opponents buy and what's in their deck. What you don't know is the order of their deck.
Check out the boardgamegeek.com entries for each game and see what people are saying there.
Personally, I enjoy Thunderstone much more than Dominion. Innovation has it's own place in my collection that doesn't compare to any other game I have (yet).