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I definitely think that making the magic system separate will help stretch the game longer while feeling better:

Being able to do all the books at the start kinda feels overpowered on the various runs I done, especially being able to get them from the crates at the start in the school (which feels weird because I thought the school was supposed to be some pocket from the rest of the galaxy). Being able to "unlock" the ability to use spells by using juice in a more tiered manner would feel nice and add more variety to the leveling system. This could be done with two ways-

  1. A more player controlled approach, with them basically learning to "read" the book by spending juice, this could be done for every weapon by giving the books each debuff and buffs depending on how good the player can "read" the book. Giving it half damage at a low tier and then giving a "crit chance" or "greater damage percent" would help not make it to where one stat controls all the magic, which would probably be liked because people also like being able to tweak the various physical aspects of the characters, so why not the magic system?
    1. Don' know where they would spend their juice at, perhaps a different fountain or a new NPC?
  2.  Giving books a "unlock more power by completing certain tasks" which would make it more story/tasked driven. You would probably have to make it more of a binary system with just "you can't use this because you haven't explored/killed/helped [X] yet" (or a more subtle hint what to do).  
    1. This could encourage exploring or progressing the story, but it may make it feel to gated.

HOWEVER implement anything like these two things would make a lot of extra load with every new spell added; with the first approach suggested, you have to make tiers for every spell book and judge what would be the proper costs for each; with the second approach suggested, you have to make story beats and/or tasks kinda connected and judge what time accessing the spell would be that complements the average gameplay.

Really you can just ignore this because it would make a catastrophic workload for you, but with how the spells work now just shows me that it needs to have some limiting factors from the get-go and that it needs more tweaking of it's properties like how you can tweak your swing speed and damage with melee weapons and how you can tweak your movement with jump, fly, and movement speed.

I'm still going to be happy with whatever direction the game takes though with its iterations, hope the game-making process goes smoothly for you! (it's your project after all, not mine) ((also sorry for the horrible grammar and run-on sentences))