I was tempted to make a weapon/evolved weapon tier list yesterday for hard mode. They'd be measured on their own merit with their addon (if any). There are just some of the weapons that transforms too drastically with other addons:
The Qigong (blue firebolt) attack when upgraded is an alright monster thinner attack, making the job easier for your turrents on the late hard waves starting at around 27minutes. Effectively a high C-low B tier weapon depending on your situation.
With the durable genes upgrade (increased weapon duration) it does around double damage. On a crit build the damage is further multiplied. With lowered cooldown it's sort of multiplied again in that the attack speed is increased. The addon needed to upgrade doesn't synergize with the weapon itself and people could scuff at it for this "anti-synergy". What the addon does synergize with is the auto-cannon-turrents (Gatling Self-propelled Gun). These weapons form an amazing defense together. The upgraded auto turrent is probably a high A-tier weapon, while the transformation of the Qigong attack with the other addons and what it offers it "partner" makes it a low A tier.
Seeing the weapons and their upgrades as isolated entities would be a mistake. Except for the "Storm Missile" weapon. It's the best and stand on it's own as an S tier weapon. Looking at the other side of the coin we have "Terminate Ray". It's definitely the strongest weapon in the game, but the addon required will likely screw over your run past the 27 minutes mark on hard mode.
I used to see the "defense radiation (laser bots)" as an A tier weapons, but their low range really let's them down. It's probably more accurate to have it be in the C-B tier.
The upgraded black holes are in principle better than the Qigong/blue firebolt weapon, but the addon is in my opinion almost completely useless. Most of the weapon/addon level ups aren't from XP gathering. They come from the elite drops.
People haven't show much love for the support missile weapon and it's upgrade. It's really strong when you use it right:
I currently like the second character the most with her increased crit chance/lower cooldown and she starts with the blade.
My own personal weapon priority considering I already start with the blade is:
1. Fast fire missile.
2. Auto Cannon.
3. Sawblade/blue firebolt.
4. Orbital laser... or just the crit on it's own.
5. Either assault gun or shotgun.
6. Whatever I need in the setup or screws me over the least.
A little tip. Besides looking at the manual. You can see which addons are required in the item menu to evolve a weapon as it's placed right under the weapon (with an exception of the bombing missiles alpha and beta who combines with each other and not the speed addon: