well, that was fun. super easy, but fun.
i currently have 0.51 downloaded (too lazy to update until some more major changes) so idk if it's any different in 0.53, but...
it seems you gain +10% damage every level. so by the time you hit level 100 you are doing 10 times as much damage. that is WAY TOO MUCH. personally i would nerf it down to +2% per level AT MOST. then it's "only" triple damage by level 100. (no matter how much you nerf it, you're going to end up overpowered by the time you hit maximum level. it's just a matter of trying to keep it "reasonably" overpowered instead of completely broken, e.g. not killing cyberdemons with 6 shells when you can carry 500 of them.)
also once you hit a certain amount of maximum energy, your EP regeneration is fast enough that you can literally stay invulnerable forever. of course, by that time you don't even really need it since you'll have a ton of health, basically infinite ammo, extreme damage, and probably a massive stockpile of medkits and armor, so you're already basically unstoppable anyway. maybe replace the invulnerability skill with "half damage" or something instead.
also chainsaw marines are way overpriced. they're effectively chaingun marines with less range, why are they MORE expensive?
credits are kind of useless (except for getting weapons earlier than normal but doom 2 gives you everything in the first few maps anyway- you can have a full arsenal by map08)
maybe they could be used not just for purchasing items but also unlocking skills and upgrades? like, start off with just the "lesser healing", "fireball", "shop", and "unarmed marine" skills (for example) and have to buy the rest. this would also be a good opportunity to add some more varied abilities, particularly in the projectiles category.
alternately, have a few weapons and items that can only be obtained through the shop.
speaking of credits, once your rank discount gets high enough you can actually generate credits by buying armor and then breaking it down for more credits than it cost. this is not actually very gamebreaking since by the time you get a high enough discount you'll likely have a ton of credits that you don't have anything to spend on anyway, and it's still really slow since you have to pay 50 EP for each broken armor and another 50 EP for each shop visit. i would recommend lowering the discount so that max rank means you have a 50% discount instead of 95%.
honestly, the real problem is that doomguy is already way overpowered by default. if you were to start out slightly weaker than normal and not gain as much from each level (or have less levels), it would be more fair. it can hard to balance "fair" with "fun", though, so don't go too crazy with the balancing.
this is a great effort so far, though. just needs some fine-tuning and more content (not TOO much more content; feature creep can derail a project surprisingly fast)