My thoughts on the weapons.
Matilda, Kendo custom Samarai edge, M19, SLS60, Quickdraw Army, JMP HP3 - These weapons are seem to do the same damage, same rate of fire minus the quickdraw which is still balanced because of slow reload... This would be a 6 way tie to me.
Yes the 0.45 and 9mm in this game seem to be on par for damage. Notice you dont see 9mm in B scenario unless you make it. This is a difficulty designed into B scenario to give the player an additional struggle.
Matilda with all upgrades - waste of space. better to use matilda with extended mag and compensator, no to the 3 round burst stock plz.
JMP HP3 with extended mag - great side arm for Claire. I always use this over the SLS since the reload is quicker and I prefer less reloading. Damage is the same.
Shotgun vs grenade launcher - I would prefer shotgun over almost every other weapon in the game. In its base form, the W-870 kinda sucks when you miss a 1 hit headshot but you can instakill all "sleeping" zombies which is wonderful when you have to run from X later in the station. W-870 is really worth taking two slots for the full upgrades. The trade off is, its terrible at killing lickers. The Grenade launcher on the other hand is wonderful for killing lickers with flame rounds. Most of Claires scenario, I would save as many flame rounds as possible as it seems to deal more damage in a short period of time. You could perma kill plants (2 shots) and lickers (1 shot). The acid rounds on the other hand are extremely lackluster. I still havent figured out the strength to using acid rounds. It made be better for boss fights, Damage over time is extended and you can easily switch between weapons to deal additional damage while DoT is ongoing. Both flame and acid rounds are terrible vs zombies.
Lightning Hawk vs MX11 - This is a no brainer. Lightning Hawk wins in every category. Damage is high, can 1 shot zombies, 3 for lickers unfortunately (sometimes 4). MX11 is only useful for stunning or de-legging zombies to run by. The real benefit of MX11 is the silencer upgrade allows you to shoot it around lickers and Mr X (next room, havent tested same room yet) without alerting them. The 50 round extended mag for MX11 is useless except for getting some extra ammo. In hardcore, extend mag should be skipped everytime.
Sparkshot vs Flame thrower - This is tough. On one hand I love the range of the flame thrower and that you can kill a whole row of zombies at once, but it doesnt stun enemies so its useless against bosses and stronger enemies unless you previously stun them already. Flame thrower destroys G2 and G3 when they go down on their knees. Sparkshot requires some skill since you can acccidentally fire through your full ammo by accident. When it does work, its great for getting past G adult creatures and eliminating Ivys and lickers. I love using the spark shot on G4 as it does deal damage over time and stuns very well. I would place sparkshot and Flame thrower as a tie.
Minigun vs Anti-tank rocket launcher/ATM-4 - I would put these both as a tie as well. Love the rocket launcher as its a 1 hit kill weapon for almost everything. Minigun is a blast to use as well. Theres really no need to compare these as you dont see them all game until the last minute or so. The infinite weapons are fun but I cant judge them.
Side-Character specific weapons :
Ada and Hunk handguns. The MUP and whatever Adas is called are tied with previous mentioned side arms. same damage, same fire rate, same reload speed. Hunks has more ammo per magazine but that doesnt matter much.
Hunks MP5: As much as I like using it, its the same as the MX11 but with no upgrades. Nice that it has 32 rounds instead of 24 but rate of fire and damage is about the same as MX11. The reload speed seemed slower too.
Final Verdict: Out of all the weapons in the game for use and versatility. I perfer the fully upgraded shotgun. You get gobs of ammo for it, 1 hit zombies and dogs, decent damage against boss fights, you may not be able to kill an Ivy but you sure cant miss a bulb blasting him in the chest real quick.