Got a few suggestions id like to stick here, some are hopefully simple, and or food for thought.
1: iv noticed maybe 1 area 2 at most were some of the key cards don't have there color coded base they hover on under. most if not all have some color indication under them, minus a select few.
2: this one is a potentially crazy suggestion, you know in unreal how the dispersion pistol can be upgraded over time, or how each mission in unreal 2 you would get a upgrade of some sorts from Issac, i was thinking that what if each guns secondary fire is something you acquire after killing a boss, that way you can deliver every gun to the player, but then they still have a secondary fire to unlock some how, maybe after each episode ends? or boss kill, as there is only 6 guns in the game with alt fires, 5 if you don't count the shotgun, and you could have that as is with its secondary fire to teach the player there will be one. and there are 5 bosses = 5 attachments after each kill, you wouldn't have to change the models or anything. maybe each boss drops the attachment and that is how the mission ends vs on kill, collect it with little top left green text then mission ends. again this is just a wild suggestion. not something that has to be done. just spit balling :3