Thanks for making this guide. I wouldn't have framed any of it as "this is the right choice, this is the wrong choice" though. Everything has its place. Except maybe In-flight Mobility and the Pistol. ;)
If you watch speedrunners, you'll see they use a small stable of splash damage weapons, switching quickly from the Explosive Shot on the Combat Shotgun, to Lock-On rockets, to Missiles on the Heavy Assault Rifle. It keeps them from running out of ammo for any one weapon, and the cooldowns on each recharge while using the others.
Most people, though, just run into combat holding the gun they were walking around with. They also pick a favorite, and stick with it. Early weapon choices have more to do with number of upgrade points and mod availability than anything. Markiplier's playthrough is basically nine hours of Explosive Shot, which is the very first thing you find.
Personally, I used the Plasma Rifle the most, and I am a big proponent of Heat Blast. The gun does great damage to begin with, but when mastered, also gives you a free 110° Super Shotgun blast every 24 shots, or every 10 seconds even without firing. Suddenly those slippery imps dodging all over the place and trying to melee you doesn't matter, anything less than a revenant is one-shotted, and anything bigger is stunned momentarily (not staggered). Side note: you do have to have at least 1 energy cell for the mod to charge automatically via its mastery.
Citing most of the runes as underwhelming and then lauding Saving Throw is odd. What about not dying to begin with? Seek and Destroy II gives you the mobility of a summoner, and lets you zip thirty feet into the air to glory kill cacodemons. Blood Fueled makes you run as fast as a charging Pinky. The most damage-per-second you can do with a standard weapon is with the Mobile Turret mode on the Chaingun, and having infinite ammo via Rich Get Richer definitely "makes the game easier". In fact, it becomes almost trivial. I had to stop using it.
Anyway, it's best to keep an open mind and run through multiple times trying to make use of everything. The game has a lot to offer, and the different guns all benefit from different runes and playstyles.