Thanks for the feedback!
Yeah, the strategy portion is always a hard thing to tune. Especially with a limited time frame, like a gamejam environment. I think it may need more practice to get a better feel of balancing.
Regarding some explanation of why you are losing abilities - the game is essentially an RPG played out-of-order in terms of storyline. As a result, you gain upgrades when the storyline time moves forward, but you are essentially losing upgrades when the story progresses backwards. (Like, if you choose to upgrade X ability in chapter 9, you no longer will have that ability for the previous chapters)
Obviously, I need to work on a bit more on explaining it better in the game though.