I'm not trying to insult you or any of the other Devs Rarebit, but..have you, kinda..looked at the topics in the forums?
I mean, I've seen at least 3 good ideas that could be implemented. Truthfully, (And I haven't been here that long, but I have read about the Arcs) a reboot of the system should be given, in which the Matrix (not all of it's inhabitants) are rebooted and a clean slate is given. Take away all this crap about Cyphs, and make them what Cypher was. A man who wanted back in. Make them help the Machines, make them want to be in the favour of them, so they can be reinserted..Make EPN someone who wants to follow Neo's dream of a world with no limits, a world with choice. Show us that Morpheous is dead and gone, show us that Neo is trapped somewhere, and he needs our help, show us what The Matrix can be!
Right, now here's how I'd do it (Not that you will or probably want to but meh)
Clean Slate - A crash in the system reboots everything, fix the issues in a way that you can dea lwith them one at a time, a system restore. Then take one issue at a time.
EPN is not a sub org - EPN is a group that believes Zion is not doing everything it can
to continue Neo's work. They live in Zion, as they will work with them, but it is a strictly professional relationship. Give them a new Operator, if Link doesn't want to join.
Specific missions/Live Events - Make Live Events link up, with one part going on for an hour or so, in which you are looking for something/someone, effectively a "huge mission" Sarah Edmontons (sp?) for example, the issue was never resolved. Make EPN look for her, focus on them, sure the other Orgs can be in it, but focus on them. It might be their *CENSORED* Messiah for Neo's sake (Editors note: Couldn't help it) they would be on the frontline looking for him/her. That is only one of many.
Games for players, by players - Sure most people here may not be graphics experts, but perhaps put together a team of players who have good ideas that could be implemented into the game (i.e Missions, New Content)
The Games Engine - Surely SOE can afford to borrow/buy a technician from Monolith that could help with the game engine. It's obviously within their money to do so..
Online Expansion/New Content - It's been 3 years, surely you can add in more fighting styles, or at least combine fighting styles. Jeet Kune Dow (I believe that's how you spell it) would be a great addition, or at least make the combat more believeable. I'm an Aikido practicioner, and from what I've seen (Videos and other players responses) there is no true Aikido combat in The MxO. Aikido is a defensive Martial Arts, specifically used to immobolise or disable your opponent using grabs, throws, pins, and other things. There are stances, and ways to defend yourself. Maybe don't implement them all, but the very basic stances that deal with shoulder, neck, face/head and body strikes at least.
Ikkio
Bonuses: Added defense to lower half of body, lowers defense of upper body.
There's an example.
Graphics - I know it's hard to make a perfect HD experience for online play, but at least have a small team dedicated to that and the weather mechanics of the game.
Advertising - Again, no money issues here, SOE could easily advertise The Matrix Online on the internet, and in game. I mean WoW has Mr.T, Shatner, and other celebs doing it. Get whoever played The Kid to walk onto the screen, with an offering of the blue pill, or the red pill, and some game play (A mission run from some players who roleplay during their missions)
Sorry for the longish post, but I truly believe that this is in the grasp of SOE, or whoever handles the *CENSORED* game...