I think atleast some of the following changes would make Bootstrap Island stand out even more and be even more realistic than it already is, while simultaneously playing into the survival and bootstrap aspect of the game making the player have to manage even more stuff which could prove a nice challenge especially for those already adept with the games current mechanics.
Ability to de-cock the hammer by first grabbing the hammer and then pressing the trigger to free the hammer, allowing you to slowly move it back to its de-cocked or half-cocked position.
Functional flash pan: Allows and in order to shoot requires you to open the pan cover without moving the hammer to allow you to pour powder in the flashpan in order to make the reload more engaging and realistic. (It would also be cool to be able to later open the cover in order to pour out the powder for whatever reason).
Functional ramrod: Allows and requires you to extract the ramrod from the gun(s) in order to ram the ball into the bottom of the barrel instead of the current state of just dropping them in with seemingly no friction from the barrel stopping the ball from going deeper.
Flintstone erosion: The flintstone will erode after hitting the frizzen for a couple of times, causing it to go blunt and either needs to be replaced (perhaps you could get a new piece of flint by striking a rock against a stone surface) or knapped again with a knife for instance, in order to maintain the guns functionality.
Barrel fouling: Hard and corrosive residue is left in the barrel from firing the weapon, causing it to be harder to ram the ball in (if the ramrod would be functional) and eventually just making the gun unusable (because you cant load it and firing it could end in disaster if somehow already loaded) unless you were able to clean the barrel with something like a damp wad of cotton (maybe you were even required to dip it in some sort of solvent) on the end of a rod of sorts.