We've already got Visual Novel Mode, so how about the opposite, let's call it Free Battle?
In the interest of not spoiling the story, let's say it's unlocked after finishing Story Mode (can just skip through visual novel mode if we're impatient to unlock it). Now, from the main menu, we can choose "Free Battle" and get taken to a Deck Builder. After making a deck or two, we can now choose to fight any of the main story and side mission AI decks. This would in itself be really cool for those of us who just want to jump straight into a battle, and for testing out combos and new decks.
If we want to make a bit more of it, let's say we earn stars for each victory to upgrade our cards all over again. In order to unlock some more interesting cards, say the guest cards (Kaden, Galina, etc.) or even some AI cards, we make a few new boss decks that have to be cleared before the cards are added to the Deck Builder.
I'm predicting this will be requested by Steam users anyway, so I'm just ahead of the times.
Replaying the missions with a custom deck is something I already had in my testing system, so that's relatively simple to do.