When deckbuilding, I often think that a certain card might be great for a deck, but for whatever reason (mostly not owning the card at the time), I replace it with another one. That can be hard to keep track of, especially in a commander deck.
I was thinking about adding another item t the right-click menu of cards in the deck, where you'd be able to set a replacement card that you actually use instead of the card listed - possibly even with multiple cards. Since a simple text field would be enough to store those, I'd make it a general per-card note area that allows you to set a short text, which could be displayed simply after the card name, automatically written in parentheses, like this:
4 Temple Garden (Elfhame Palace, Selesnya Guildgate)
2 Chained to the Rocks (requires Mountain)
Not sure how easy this would be to implement, but at least the deck file structure seems to support things like this very nicely.