The two other card games with changing formats that I follow, Hearthstone and MTG, do it in very different ways. Hearthstone just slams all the old cards in a corner and says “bugger off” to their Balance. MTG, on the other hand, handles it in a much more interesting way.
In MTG, set rotation has lead to the creation of many new formats, like Commander (the CORRECT way to play MTG). It uses the fact that the game has old and overpowered cards to expand on gameplay by letting these cards be played in more controlled environments. However, MTG is a physical card game which gives it an advantage in that playing with friends is a large pet of its appeal, so it does not have to try too hard to be mechanically good. I would love to see novel formats in Duelyst that are not just “same as standard but with different card set.”
However, I’m not sure if Duelyst has a large enough community to support multiple formats like MTG. Fun formats in the art can become barren wastelands if not enough players catch on. And if a format has little people, it will continue to shrink in a positive feedback loop.
Personally, I would love to see something like MTG’s commander format in Duelyst, where you get to choose a legendary minion as your general.