well, that last ability is utter unrealism. doesn't really seem like a good idea. the other one isn't very good either. that way, you could just use the ability, press g to quickly let the three minutes pass, and move on to use the ability again in the next fight. however, the fact that you can only use it twice could compensate. still, you usually don't have the oppurtunity to fire six shots after each other. either too few enemies, or too little time.
what would be the purpose of those guards? besides that, 500 men would never fit in your small settlement, and you could never fit them on the screen. sure, you sometimes get attacked by natives, but those can be easily managed by yourself or 5 regular AI people/3 with good skills. although it may be more.
the shop idea was more or less what i suggested. simply have the same guildings you would have in any town in your settlement. however, i think this would make the towns in your chosen island largely unnessesary. you could simply go to your own store all the time.