I don't have any criticism for this one, is really good, easily in my top 3 of your mods, but I have an idea, but since I never seen something simmilar I assume is a pain to make so I'am not asking nor expecting it to be implemented, I'am just throwing it on the table.
The secret weapons mechanic is really cool but sadly you can't carry them through pistol starts, wich is obvious but I like pistol starts and I like the secret weapons, so my idea is having an option "balanced pistol starts" that lets you carry secret weapons through pistol starts and only the secret weapons, ammo and normal weapons you go to square one each level.
But as I said I never seen that before so maybe is just impossible to do I don't know, game dev was never my forte.
Anyway, another great mod by Cosmo, even Terminus thinks is cool as hell so I can't say bad things about it even if I had any to say.