What I'd suggest is the following:
1. Remove the current disintegration system entirely. It's not fun, it's hard to balance, and it's not particularly useful. Unless you've got a few dozen identical blue weapons that use it in Part II, that is.....but I still think this is a bad mechanic that needs to be retired.
2. Add a replacement system, tied to the nano damage type.Nanites degrading things into their base molecules makes sense for a special status effect. And this wouldn't be a blue flash of death. Instead, it would be damage over time to the affected segments. This would be a stackable effect: getting hit a lot would increase your problems up to a certain amount. Use the 1-7 scaling system so you can control how long the effect lasts (or how much damage it does?). So in effect, it's a combination of the radiation and organic acid effects. If an armor segment is destroyed by the status effect itself, disintegration would either kill you with a nice dissolve effect that isn't blue (so that weapon colours aren't restricted), or leave you on 0hp on the affected armor (and end the status effect). Thus, it's a terrible thing for a no-shields ship....but it's not that terrible. It should also work on stations and wrecks, destroying them exceptionally quickly by draining HP.
3. Add counters in the form of regen barrels, solvents, and other items. Because having counters to DoT status effects when they're introduced is not something this game has been good at in the past. And it's important to have a counter, particularly as this would be a very rapid, high damage effect. High-mass armors could be resistant to disintegration (chance to avoid + slower HP drain if you do get it with no change to duration), and the existing immunities would still be very valuable for preventing it......but armors that have no resistance (or a vulnerability) wouldn't be instakilled regardless of HP.
4. Remove the Iocrym Disintegrator, and replace it with a new weapon with a similar name and brand new non-blue effect that uses nano damage and the new disintegration.
5. Rework the Gaian Demolition Cannon to also use nano damage (current damage level is fine because it's terrible. THe DoT effect would make it very dangerous, but hard to use) with the disintegration effect. Remove that nonsense on the description about mysterious energy sources, and have it be recharged through the use of a barrel of degenerative nanos. Add these barrels as an assured drop in Gaian dustbins. Thus, the gun actually makes sense for the first time ever. #SavetheGDC
This would add the nano damage type to Part I, give us a nice introduction to it, and also rework a status effect that's been troublesome for many, many years. The Q-sphere is iconic.....but it's not worth wasting a good status effect over. There's a lot more that can be done with disintegration. Rather than an instakill that messes with game balance (and makes no sense since that makes two instakill specials), let's have it be a top-level equivalent to radiation, with possibile utility in Part II as a low-level hazard as well.
