What I would definitely want from Goonchem is a) temperature chemistry, and b) the base idea beneath chem effects (that is, some prob() based stuff and some HP-gated effects) and side-effects/chem interactions.
Trekchem, however balanced or not ATM, is boring as shit because it is shallow and extremely predictable. I've played with organic chemistry IRL and even with the simple stuff I could do it's never as clean, quick, reliable and safe as SS13 chemistry. And the Chemist winding with a faceful of broken glass and hot liquid is as entertaining to recount as Viro or Toxins fuckups, without their round-disrupting powers.
Addiction itself could be tweaked or removed completely - that's the wonder of open-source development.
Ghetto chemistry can work even better than it does on trekchem - trekchem's problem with ghetto chemistry is that it's simplistic enough that there isn't much room for improvement in actual, sterile lab chemistry over ghetto chemistry. /tg/, at least, has the machinery improvement thing, but Baycode doesn't.
If the problems you mention are present, it's far more because coders are short on fucks to enhance ghettochem - which could be addressed by adding base chems to some commonly available items and adding alternative recipes, adding a rough and unreliable ghetto chem heaters in the form of, say, welder-ing a bottle, and allowing grinding/washing out/whatever patches, respectively - though, to be fair, the newchem project is mostly Goofball's brainchild, so...
I'm not saying Goofchem is good, necessarily - but it has some nice features that could be ripped out of it.