I haven't read it all, but I really admire Madvillains patos and genuine care for this game and the factions.
I think your interpretation is wrong though. I know a lot of people sit around and reminisce over faction leaders of the past and how everything was so great, and that the server population now sucks. Have you ever stopped to consider that perhaps the current server generation isn't so interested in factions because the factions and its players don't stand out as those beacons of lights that once attracted you guys? I.e. rather than blaming those of us that have no interest in joining a faction (but still likes RP), perhaps ask yourself what your "ikons" did to draw you guys in back when you were new? There's generally an eagerness for new players to create their own factions alongside the official ones that represent the ID, and I think that says a lot: They basically want the same thing, but feel the official factions can't provide that for them so they create their own. If I was a faction player, that would really be food for thought for me.
I think transparency, and I mean real transparency, would restore some faith in factions. It is so easy to get the impression that a lot of factions are run by a handful of people that settle stuff on skype and so on. I have had some negative experiences in my time playing RNC for instance and I have been blamed for many different things by players who play in different factions - they heard all sorts of bad things about us, most of which aren't true, and that all stems from faction skype chats (or so I have been told by people accusing me of wrong-doings). It's frustrating having to defend oneself against something you have never done, even more so when you know this "slander" only exists because the power-relations in this community are skewed towards a small circle of players with influence on factions (their own and others) and admins. Yes, I even had an admin uncloak next to our group of RNC ships, first telling us we cause lag and we should feel bad (even though none of us were firing our weapons, and the server was having a lot of problems with the jumphole bug - but naturally our idle green ships MUST be the ones creating the lag, right?) then trying to goat us into making oorp comments in regards to his admin ship uncloaking in our face. Said admin apologized in PM's later, but it's a symptom of what is wrong: The entire system is corrupted, and nobody has the strength to rise above it.
It seems like a closed world, and as an indie player you are met with the attitude of "join up or you suck!" That might work on the weak-willed or kids, but for most of us we feel affronted - it's a sure-fire way to run off potential members for good. That's why I think the idea of "fakshun players dictate the RP" is very bad - a lot of us just aren't fit for that kind of power (perhaps you are in your own eyes, but that's not how it's perceived by a lot of those players who aren't given a voice), and there's no checks and balances save for yourselves. It's an unhealthy situation for the factions, as well as the indie players.
You need to open the faction system up, be inviting to more players, and not take the douchebaggery to the next level. You still hold the most vital selling point: In Disco, gank is King and noone can gank like a faction with high numbers of dedicated players. Joining a faction most likely means dying less and killing more - two things a lot of Disco'ers fancy. Plus you get the privilege of being treated as an equal and actually RP'ed with by some of those players who "dislike indies". Try to kill off skype and use the forum and the game, where transparency and accountability is ensured. It's a law of nature that in the disco universe that any power that can be wielded will be wielded. You are very much on the wrong path if you think the answer is to give factions more power.