Will some of the expansions reintroduce the more complex features which were written out of the original design (like adding cards that introduce more of a deck engine element into the game)?
I think that Mike hinted at that in his article. Ah, here's the line:
Mike's Designer Diary wrote:
They were also just one more thing that was confusing to beginning players, so all of the straight global effects got moved out of the base set.
With the part I bolded, I think it's pretty obvious that Thunderstone will have more complex mechanics in expansions. If you read any of the Dominion diaries, Donald X. did basically the same thing.