Since Devil Deals are such a huge aspect of Isaac, I thought it would be super cool if they got represented here too.
How I imagine they'd work is if you clear an area without losing any chargers (since that's sort of like taking no damage), after the shop, you get a special Devil Shop with a selection of 3 items with prices of a different sort: Game Modifiers. Similar to the Chaos boons in Hades, they temporarily handicap you in exchange for a more powerful upgrade. Handicaps could include things like Curse of Darkness, Curse of the Blind, Hearts don't fall from the sky, shovel gains a charge, etc.
Of course, the items from the Devil Deal would be stronger or more useful than the average shop item to compensate. It would be a great way to implement additional slots if you don't just want to give them out after the boss fight, as others are suggesting. You could also feature stronger babies like Lil' Brimstone or other strong passives worthy of the trade.
I think this'd add a great additional risk/reward element to the game which rewards skilled play, as is the case in og Isaac. Just wanted to say your game is awesome and I've been loving playing it!