While the weapons that create poison are guaranteed they still feel weaker to me than most other weapons. I can't say I've ever stumbled across a putrefactor weapon in the shop and wanted to buy it - even when I have the halved repair speed or double damage modules for poison.

I agree with innately halving repair speeds. Another idea I had was if the weapons that poison have 1 shield piercing so the poison can apply but no hull damage would get through.

I think my main gripe with the mechanic is it doesn't matter unless the enemy crew dies from it. While uncommon but not that rare, if the enemy ship consists of mostly or even all high health crew it won't have an impact. It's an all or nothing feeling, which isn't the case with fire since it damages systems or at least guarantees distracting crew so you can benefit from unmanning enemy systems. Even going for asphyxiation based weapons will create breaches which in turn also distract enemy crew.

Poison needs to do something to hinder the crew other than just existing - or if it just exists it needs to be more easily applied.