Now you've just given us more to reply to... :hmm
bool AUTO_AIMED_FIRE = true;
Agreed, remove it.
bool USE_REAL_CANNONS = true;
Arcade OFF, Realistic ON.
bool ALLOW_CRIT_FROM_BALLS = true;
Agreed, move and keep default setting.
bool ALLOW_FIRE_FROM_BALLS = true;
Ditto
bool EXTRA_HIT_CHECK = true;
Arcade/Realistic toggle.
float CANNON_RANGE_SCALAR = 1.0;
- AND -
float CANNON_DAMAGE_SCALAR = 0.5;
Both can be removed.
bool CANNONPOWDER_MOD = true;
Probably Arcade/Realistic toggle.
float ARCADE_MULT_CANNONS = 0.5;
Move to internalsettings.h.
string BOARDERMODEL = "standard";
Agreed, I think some of them cause problems. Remove the option, I say.
bool RANSOM_PRISONERS = true;
I don't know about the OFF setting for this, but merging it with the other setting sounds good.
bool FOOD_ON = true;
Probably Arcade/Realistic toggle.
bool AUTOHIRECREW_ONCHANGESHIP = true;
Might actually be worth keeping, maybe as an Arcade/Realistic option?
Or perhaps 'Iron Man' instead, only for players who want to do everything themselves.
bool SY_RPG_STYLE = true;
Arcade/Realistic toggle.
bool REALISTIC_SHIP_PURCHASE = true;
I've never really paid much attention to this one. It does sound like an Arcade/Realistic toggle to me, but I think players should be given a fair warning.
Think about all those who keep asking "Where can I get this ship?"...
Then again, considering that point, maybe the toggle should be left alone, OFF by default, and perhaps ON by default in Iron Man Mode.
bool IT_RPG_STYLE = true;
Same as SY_RPG_STYLE.
int SALARY_MULTIPLIER = 3;
Yes, keep it.
bool KB_TUNESHIPS = true;
Agreed, remove it. Upgrades are a must for serious sailors!
bool CANNOT_RELOAD_WHILE_FIGHTING = true;
"Your gun won't reload gun..." Hang on, that doesn't make much sense.

:
I say Arcade/Realistic toggle.
bool ENABLE_AMMOMOD = true;
Arcade/Realistic toggle.
bool BLADEDAMAGE_ENABLED = true;
Agreed with link to Weaponsmod.
int CORPSEMODE = 4;
Agreed with keeping, but do the numbers go '0,1,2,
4' on purpose...?
bool AUTOLOOT_ON = false;
Agreed with keeping.
OK, that's a whole bunch more done, how many more to go?