Couple of answers:
- Sniper Rifle - Snap Shot isn't useless. Think Reaction Fire. Sniper Rifles with high ROF would obsolete all other firearms.
- Repair/Refuel/Rearm order - I cannot modify such things. But if player had a free choice here, the flexibility would perhaps be too great (ie. I've never encountered the problems you're describing in my playthroughs, since I've tried not to abuse Bonaventura so much, and most importantly, to never get damaged when low on fuel).
- Maps: I've checked that ship map in mapview and everything seems to be in order. Engine limitation? As for terrain map errors, it's Hobbes' terrains, not mine, so please contact him (mine are only ships and Pirate Hideout).
- Cyclops - they're simply unfinished.
- Flamethrowers - various people say various things but I am not sure if they train accuracy - I'm not sure if arcing shot weapons can train accuracy at all.
- Stone hatchet - would you please stop beating this dead horse?
- Radar Range extravaganzas - no I can't mod that.
- Stat tracker - it is an .exe modifier. I'm already using an .exe modifier. I'm not learning how to compile code out of sudden now.
- Research/manufacture Popups - I don't understand how they work and when they appear, and when they refuse to and why. Although I can assure you you DO GET everything intended. If there's no popup, looks like I'm not doing this the proper way. But oftentimes doing it the proper way would make it impossible to do it my way (ie. to give the player the exact things I want).