I'm pretty sure solving all the problems at once gets you on the consideration list for a Nobel Prize (why they established a Nobel Disco-peace Prize I still don't get though).
Off the top of my head, various issues that seem to be related are as follows:
The belief that Factions are trying to destroy Independents and that Independents are trying to undermine Factions. If this could be resolved, I think a lot of animosity would go away. Not even sure the root cause of this.
The belief that certain members of the dev team are amazingly biased and/or out to get you. Not sure a fix on this, but having more clarity on matters would help. Justifying through the use of pure numbers isn't always helpful, nor is the fact that there doesn't seem to be much saying how things are done. I think if such was the case that a lot of the conspiracy cries would go away.
The belief that admins are out to get most everyone. Ok, this probably wasn't helped by the recent chaosthread related chaos. Some other examples are people who are complaining about various rule infractions, but unwilling to do anything about them because they think everything they say on the matter is ignored. Another is that admins unfairly ban certain people.
Solutions? Good question, again. For the latter specifically, I'll go back to my previous idea from quite so long ago - all sanctions and rule related posts should be done by a common account. Then it steps away from any feelings of it being personal (away from, mind you, not completely separated from).
The Admin team also seems to be getting overworked again. Several new Admins had been added, but at the same time there's been an outflux (why isn't that a word?). Perhaps that matter should be looked into? Many hands and lighter work and such.
The rules nitpickery. People have a tendency to microanalyze all the rules. Why? Dunno, I barely passed Sociology, but I figure I may've gotten insight if I paid attention. A complete revision may be in order, possibly with examples of right and wrong. There are still a couple rules that seems obsolete, for one thing. Streamline the rules and it may decrease the amount of analyzing the mammoth situation, with rules added on top of older rules, etc.
People being angry with unnecessary force. Again, another hard to pinpoint problem. Lots of people get it right, but lots also seem to get it wrong. Joe's last thread on the matter shows a lot of the opinions. I think the fact that there IS a division enforces the problem. Finding a middleground is a must.
The feeling of powertrading and people acting oorp. The fact there is plenty of accusations here is just as much of a problem as any actual issues (which are hard to pinpoint for vagueness). Sure, there are plenty of various obvious incidents, but I'm talking about the borderline stuff - is it oorp to attack a fighter in your freighter? There are opinions on both sides. Is it oorp for a Zoner to visit Station X? Opinions are, again, divided.
And where is the line between trading and powertrading? Certainly people can come up with examples that are clearly one or the other, but a huge portion falls in the middle. We need to find a way to resolve these in a way that doesn't further divide people.
For the Zoner specifics, Dab's recent thread has a lot of interesting discussions on the matter. It seems it may be being worked on by the community. It's a first step at least.
A difference in the view of the overall goals in Disco. Many people seem to want a static situations where others want something dynamic. I don't think I've ever seen a post about the overall philosophy of Disco in this regard. Which way does it lean more? Certainly that can help move things forward.
Basically, the best solution to the problems that I see is, well, actually having non-flamey discussions with particular guidance based on what Disco's ultimate goals are. The non-flamey part is hard to come by, though, unfortunately. Perhaps we could elect some sort of committee to work with the in charge types and represent the community as a whole. Then the Admins can take the position of what's good for stability and the Devs can take the position of what's good for balance. Who has the position of fun, morale, and the overall community health?
Ok, I'm done with my ramble-mobile. Whew, I need a break now.