The current batch of enemies is only the tip of the iceberg.
Not all variants for the current three items have been implemented yet, so if a monster doesn't react to being hit with an upgrade item, then it's most likely not compatible with it. Balancing issues will be fixed as time progresses. Gimmick powerups (Berserk, Partial Invisibility) still remain, due to necessity, but everything else is free game. The only way to recover the reserves is to use the ones dropped from the newly upgraded enemies. The incentive to have something that isn't vanilla enemies exist is that all regular health and armor items (Health Bonuses, Green Armor, etc.) along with most ammo has been removed, and replaced with these upgrade items.
These items can be used to morph the vanilla enemies into stronger versions of themselves, as explained by this diagram.
