Yeah. I'll have purchasable ammo packs that cat merchants will sell. that little purple thing in the bottom of first is one. You can't talk to him, but there are others you'll be able to talk to. Cion is the currency, and is what those energy crystals are replaced with.
Yeah, I always thought Cave Story beta looked much cooler than the final. also, I'm gonna have different equipment sets you can find hidden. They change your appearance and give you different attributes.
Just some advice though, from my perspective those features sound complicated to implement into your mod. If you want to lighten your workload (and at some point, I reckon you will,) consider either shortening the total number of levels, or amount of dialogue in your mod.
But if you think you can do it, that probably means you can.