Two pieces of feedback:
ONE:This
As far as more levels we did initially have 10 but as we adjusted the gameplay we started messing with the idea of it being a spacial memory mechanic as well as using resource conservation elements. The current idea is that there are 6 rounds of 6 levels and it cycles at quicker and quicker time intervals with less and less charges available. This leading you to have to balance your charges early. The spaceship moves quicker and quicker at higher levels.
... was done really well. Your risk versus reward system is good, as is the idea of resource management through level iterations. If you're looking for feedback, however, I have a suggestion regarding this which I as a player would greatly appreciate:
Your current iteration model gives players a throwback to previous levels, but you mention that subsequent iterations simply randomise which energy pods reappear, making less pods every time. If I understand this correctly, then you're not really enforcing a long-term decision scheme, you're just giving the player nostalgic throwbacks to earlier level layouts.
Try these steps:
(1) Have the game remember which energy pods a player has picked up on a given level. Leave "ghost" sprites to denote areas where energy pods have been picked up.
(2) When you return to a level later on, KEEP THE ENERGY PICKUPS PERSISTENT. In other words, respawn energy pods that you didn't pick up the previous time, and show the placeholder "ghosts" in all the other places.
(3) Finally, the crux of your resource management: the more level iterations that pass by before an energy pod is picked up, the more energy points that pod is worth when you finally do pick it up. I've already noticed that wall collisions do more damage as you go up in iterations, so to counter that you should motivate players to conserve pods (instead of snapping them all up the first time around) and "farm" them later for greater profit. This creates a (good) dilemma for the player: "Do I pick up this pod now for a small, short term reward that can help me make it through this next room, or do I save it for later, when it will become far more valuable?"
I don't know whether you'll like this idea or not: I just thought that it would be nice to marry the idea of long-term strategy with your short-term memory of a given level.
TWO:Your sound design is really good! Harness that skill and use it to your advantage! In a game where you're mostly blind, you don't need to rely solely on memory to give you clues about how to proceed.
There's been mention of incorporating enemies and other level elements. Sure, additional obstacles would be great, primarily because you can have them generate sounds to give players clues on how to proceed. Put spike walls into your game that, at regular intervals, pop out with a "schwing!" and retract with a "schuk!". Even in darkness, players can hear these noises and if they remember where the obstacles are located *spatially*, they can time their movements via the sounds to make sure that they pass through the spikes while they're safely retracted.
I'm not suggesting that you use spikes specifically (they may be a bit too cheesy for you

) but I think that it would be an idea to implement obstacles that give players audio clues in lieu of visual ones.
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I hope that this feedback isn't too presumptuous. It's just a few ideas that I, as a player, would love to see implemented.