Here's my two cents on this issue.
I've been both Omni and Clan, as most of you know, and I've attended both BoD and CoT meetings (CoT briefly). I've been a terrible RPer; I've godmodded, metagamed, and basically screwed up other people's RP plots. I've seen/done it all, and as such, I think I have a right to voice an opinion on this issue.
I agree with Trousers..a lot of people assume to be the leader of certain departments, given that they are the only affiliated person/org for the dimension, and act as such. I wouldn't go so far as to have no authority given to the players, but for authority to be given to the players BY the LTCs, as approved by ARK Events. Some ceremony and proof of the rank be given to the player, so people can't just lie about it. Perhaps it should be on a merit-based system, as in "After X assignments are completed, and given recommendation by ARK-Events, you can achieve Y level." The assignment completed requirement would to be prevent those with friends within ARK to just get merit ranks for being friends, a.k.a. preventing corruption within the system. Have certain responsibilities go along with the levels, or rewards, or something. Start the RP program over, though, and let the people who do RP and RP well shine through. Instead of letting people like me as Jermiten (I admit, I was a terrible RPer.) coming to the BoD or CoT and wielding authority, instead let people move up as they learn how to RP correctly. What happens? Less godmodding, more fun. Keep the merits within the departments; come up with good names. Have some sort of badge to prove it. Even if we get people in RP who just want the badge or the merit, they can't advance without actually learning about RP and becoming good at it. People should have to go through seminars to learn the basics of RP, or pass a test or something, so that everyone knows and understands the rules of RP.
Tacking on to that idea, I think that RP in general should maybe get a few more perks. What if each department of both CoT and BoD were able to get some sort of HUD item that portrayed a uniform suitable to the department? Have it so that it's nodrop, but requires an RP merit of "X" to use. Admittedly, some would outfits would be harder than others to design, but maybe we should have something other than Pol/AF armor, Internops clothes, or Executive suit (as far as I know, there aren't any uniforms that can be used for the CoT, except perhaps the Sentinel armor) when most of us have twinked armor anyway? This way we can come in uniform without having to re-twink afterwards. The badge could also serve for the ID that many were talking about not too long ago. This suggestion is admittedly a bit far-fetched, as it would be alot of work for the Development and graphics teams, but it could serve to get people interested in RP again, as well as make the existing members a little more prone to stay with it.
We should also be able to get something resembling offices for the RP affiliates. Since Omni-HQ is used in missions, go with Trousers' suggestion of having them in various places around the world, as would suit the department. Attempt to put them close to grid exits/whom-pah's for easy access. Other ideas would be for Omni-AF to be in the Avalon base, Sentinels to be in the Mort HQ, Vanguards to be in Old Athen, Trans to be in the building in Omni-1 Trade, etc. I would also stress having them be defended, so that they CAN be attacked by the opposing faction, but not easily. And whatever guards are put up should be set to no XP given, so that we don't have massive raids on offices by non-affiliates just for XP. Another idea would be to have an "apartment style" office; enter into a certain area, and get your own specific PF in the style of an office. Have a terminal with office-style furniture (but it has the reqs like the previously stated ID of having a certain RP merit level) so that as you move up, you can get neater stuff for the office. In a previous MMO I played, there was the ability to have a datapad set with text. I personally think that it would be immensely interesting to be able to create a datapad and hand it to someone within the office. On the flipside, that's really hard to code properly, and creates all sorts of problems for the server. It's just an idea though, if we wanted to have some phatz
Tacking on to THAT idea, have the LTC's stay in or in the vicinity of the offices, so that questions/new assignments/anything can be dealt with. At the absolute least the LTC's should be on once a week, preferably on the weekend. That way we see them more often than just once a month.
I like Dabblez's idea of having the conflict, but that gets out of hand. I know from experience that people get IC and OOC mixed up WAY too much. Just because I play a terrorist IC doesn't make me the same way OOC. Quite a few people have problems distinguishing from that. It needs to be addressed in said seminar.
As a final note, I think that there should be a way to appeal for/against a ban from RP of a player. Many affiliates step out of line, and the only thing that happens is that people (occasionally) ignore them. If there happens to be someone who is abusing RP, there should be a way to have their status revoked. I also think that their should be a way to keep OOC and IC bans separate. If someone is banned for 3 days OOC, then their affiliate status shouldn't be removed. If they are banned IC, they should receive no OOC punishment except the loss of the RP perks I detailed earlier.
That's my take on this issue.