What about something like Perks? Another single slot where you can mount a small boost that can help you in missions. They will be permanent and will not disappear when used.
They can be unlocked by reaching certain tiers, certain medal counts, buying them in a Heroes Academy, total food collected, total kills, or whatever you could come up with
Not all perks will have a drawback, but those that do, might have better effects. These perks will mostly come from Heroes Academy (You buy these with keys, and they always have a drawback of sorts.)
Also, you can only equip one perk at a time anyway, and some of them can be hard to unlock. I’d say that is enough of a drawback for those without a drawback.
Examples
Gold Digger: Slightly increased key drop rate. (Or a 10% equipment perk in results)
Unlocked by reaching Tier 10.
Voracious: Enemies have a chance to drop two food items on kill. Does not apply to Competitive Missions. Unlocked by having 100,000 food units on hand.
Bullet Dodger: 10% reduced hitbox size. Unlocked by reaching Tier 30.
Space Sprint: Slightly increased movement speed wherever applicable. (As much as a single jet)
Unlocked by reaching Tier 40.
Space Ninja: Increases your damage output by 5%. Unlocked by dealing a total of 100,000,000 damage. (Or reaching Tier 80)
Pressurized Projectiles: Makes enemy projectiles 20% faster, but you earn 10% more score. Does not apply to Competitive Missions.
Unlocked by purchasing in a Heroes Academy for 1,100 keys. (Or by having 100 Elite Mission trophies)
White Knight: You can never drop below 2 Firepower. Unlocked by killing a total of 1,000,000 chickens. (Or by reaching Tier 50)