First of all, thank you for such a helpful feedback!
I am planning a new update with the ability to start run with a different deck. With "classic" and randomly generated ones, for example. I hope this makes it more replayable.
About removing the card. I think that's a good point. I might add an option to burn the card as a reward. As an additional reward for a few coins or as a free reward instead of a new card or upgrade. What do you think?