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•  Adding indication for turrets would be great, that's what I thought, too
• I found two, but could only access one (at the edge of level 2). I noticed a door on Level 1 but haven't been able to get there.
• As for the spell usage - it indeed seems like a tricky thing to solve. The way I see it now - I'd like to get a certain "build" and focus on it, while discarding/selling/dismantling abilities that don't fit the build I'm going for. Some sort of progression for abilities could be interesting - turning unnecessary abilities into materials for the ones you need. If you have mana/health costs or cooldowns - I don't think you have to limit the ability quantity, since you have tools to prevent abuse already - you can't use it indefinitely without fighting or opening chests, which is exactly what you want your players to do. If it's too powerful - you can increase the cooldown, so you can only use it so many times per fight. Or, you might want to introduce "colored" mana/ammo that fuels abilities of the same color and is easily collectible, while abilities themselves just use the variable amounts of it - kinda like guns in Gunfire Reborn. However, mind this: right now ability charges fill a lot of space as rewards. If you take them out and make them rechargeable or permanent, you might need to put something in reward pool to compensate. Or, you can go the same way Dead Cells did - each ability is an "item" with its own modifiers
• This is of cource my personal opinion, but as a roguelike/RPG player I like sick combinations that ruin the game's balance :). Or at least find items that perform together better than they do on their own. If I want to create a build that relies on Projectile ability - I'll have to find a way to keep that ability available to me when needed - and I don't feel like I can restock it controllably to rely on using it in every combat. This is fine if you want the player to "juggle" abilities and switch from one to another throughout the run. In that case, however, there might be another problem - a player has to regularly break the game flow to get into the menu and select another ability. I personally find the idea of switching from one ability to another very compelling if there's a fun way to do it on the fly during combat.

Or maybe I'm making this whole thing up and that's not the problem at all. It might as well be how you envisioned it. It's just one player's opinion, anyway :) It all depends on how you want the abilities to be used, what is their role. There are multiple ways to do it, the solution to go with would depend on the emphasis you would like to put into them - are they an addition to the gameplay or a main part of it? What is the prefered way for player to attack in any fight? Start with this, it might show you the way