The shotgun is pointless after you get the TMD. The pistol is pointless the moment you get another weapon. The sniper rifle is pointless except in a couple more open combat arenas, where they're almost always to be found lying about. The railgun is pointless, it takes far too long between shots. The grenade launcher is actually worth having for offing larger, more difficult enemies. The autocannon is also definitely worth carrying.
Basically I beat the game using the assault rifle/weapon I didn't use until I got the autocannon. Then I went assault rifle/autocannon and used whatever I felt like at the moment.
I would definitely grab the increased damage and magazine capacity for the assault rifle, and the the faster reload for the autocannon. I'm not really sure anything else matters, because most of the other guns are so situational as to not be worth carrying. Besides which if you're reasonably thorough about picking up E99 tech, you're so positively swimming in upgrades by the last chunk of the game it gets a lot easier.