I love that idea! Please do that as an optional mode   I see three different kind of modifiers that are possible. The first one are things that makes a mission staight up harder/easier. The second are modifiers that are just for fun and the third are modifiers that change the "meta" of the mission. From a game design perspective the last categorie makes the most sense because you have to adapt your deck to that modifier which leads to a new environment with potentially "bad" card