One thing that many CCG games do is focus on newer releases by way of "seasons" and tournaments that restrict the card pool to recent blocks. It's obvious why they do this: to make money by incentivizing players to buy the latest sets of cards. But there are other side-effects: it changes the relative power-level of cards and alters the "meta" environment.
I think something similarly interesting could be done with Dominion Online by running mini-leagues or tournaments that focused on 2-3 sets at a time.
For example, we are about to see Nocturne released. It might be fun to have a tournament that emphasized Nocturne by pairing it with 1 or 2 other sets.