Benefits of an NPC system: It's a bit more relaxed, but you'd have to look at lowering some of the requirements to rank up--namely time(face it, most of us aren't going to rank up very quickly -because- of the time factor, especially at lower ranks). You don't have in-fighting(rare here, but it does exist in PC run systems) because a NPC(and by extension the staff) control the direction of the city/religion RP.
Benefits of a PC system: More roleplay, well, in theory. In the old system of favourtism, people would have to interact with the ruler/supreme in order to be considered for ranking up. Under the current system, roleplay with the leader isn't really very necessary. But, we also have the low population count. PC run also means that the roleplay of the city/religion develops by player design, rather than just how the staff wants it--which can be good, and it can be bad(bad, it goes in a direction the staff doesn't want because it totally opposes what the original intent was. Good, it can actually make the experience deeper and developed even further than what the staff originally intended). I like to think--I'm biased--that the Tyrek religion background roleplay was the most enhanced during the pre-wipe days(and technically still carries to today) because of the people at the head of the religion ... which was me, which is why I'm biased.
On the flip-side, the other religions were kind of just there, though the Mventious religions had the second most depth because the leaders of those religions were actually in-tune with the idealogy(or were chalgyr). Looking at the religions of right now, Dias and Sys'kee -technically- have the most depth, Sys'kee has a lot of room to expand and improve. Galr and Estrenal are kind of just there, they haven't really been developed because they haven't had that kind of story-telling drive. And then there's Athorien. The only reason that religion is even popular is because of the spells. There is virtually -no- background relevant RP to the religion, there's no visible flavour... it's just, "join for the spells."
So, there's up-sides and down-sides. Personally, I like having player run things... but maybe it's time we downgraded it to player-run religions and consider NPC ran kingdoms. The Kingdoms have the most developped background RP plot, because they were ingrained from the start. They don't -need- the work religions do... ... wait, am I even on topic anymore? The playerbase is just simply too small to have kingdoms -and- religions ran by players. We see this with most people just running away to Tolin. Armengar is now gone, because of the lack of interested population. Tozain and Lapis were "closed" but still remain as they were(no Sye, PCs in the kingdom does not translate to actual population >.>).
So... yeah. If we do revert kingdoms(or religions) to NPC ran, you should really look at trending some of the lower and mid-rank requirements downward. In the case of dropping religions to NPC ran, you'd have to drop the supreme spells down to cardinal as well, otherwise they're wasted(and some of them are pretty good... and some of them outright suck)