The enemy and upgrade varieties are really on point, I never felt any slight hints of repetition or tedium when I was playing. I think the addition of giving the box both melee attacks and projectiles allowed the enemies to have good diversity and have their own ways to be dealt with, for example I think the bomb dropping enemy would've been annoying due to its mild speed and decently large bombing damage area, but the projectiles allowed me to hit it for decent damage when it stopped moving, which made me understand how I could tackle them better.
I specifically liked all the details that are subtle but are just so nice to have, like how there's easily understandable markings for the upgrade/reward type before each room, or how some of the upgrades literally refer to the box character, I think one of them was "Better Tape", which just makes sense to me. Also, the settings were cool, I love being able to customise difficulty to my leisure.
I have no complaints, you packed this with a lot of content and I'm not even sure that I've seen it all. Great Work!