One thing that comes to my mind is to make only the upgrades costly (number of cards, number of missiles, amount of energy). Cards and rerolls will be free in the store. They will reset at the start of each round. This means the player will create a new deck for each round based on the information in the next level. Cards can be purchased up to the maximum number of cards. Do you think it would be better if I made a system like that?
Sounds good to me, think the difficult part will be to balance "the randomness"... think if you can fullfill the following conditions
- your main stratgey by the passive cards is most relevant
- if played correctly a "correct play" which adjust for the given level based on right passive card strategy fails only in rare cases
- you can get lucky in rare cases with the offered direct cards (just need to be rare enough to feel quite special)
it might be quite enjoyable... of course playtesting will show that it really works