PRPs are a great way to keep things active, but as others have said, you need the tools to make them as effective as possible. As called out already, Arx had a ton of PRPs during the siege, but they all felt sort of self-contained; no one plot actually felt like it affected the siege as a whole in a meaningful manner, which I think contributed to player fatigue by the end of it.
In hindsight, what I might've done there was give a weekly update of the 'state of the siege', detailing how frequent the incursions were and how thick on the ground the army appeared to be outside. If players did a lot of PRPs and succeeded well, I'd probably have the number of off-screen attacks in that report have gone down, or see a decrease in the troops encamped outside the walls. I might even have included a 'Silent Army Strength' metric, and used that for the final battles; run enough effective PRPs of people doing things against Brand's forces, and you reduce the difficulty of the final battles. Then folks would've probably felt fairly invested.
(Admittedly, I think another problem was that the siege PRPs became a lot of 'something happens, and suddenly Bringers!' and people fighting them; there were lots of well-run combat scenes, but it was almost entirely combat scenes.)
So that said, here's the things I try to keep in mind to make a PRP engaging enough to keep folks really interested:
- Players always want a chance to shine; I try to write plots such that everyone who's going on them has at least an opportunity to really do something in their wheelhouse. Every character has something they can do well—if they don't, they probably aren't going to be super fun to play forever. It can be something with no plot relevance (see: Hallie's tattoo skills over on BSGU), but there's going to be something they have. It might not even be a skill, just a particular knowledge or interest; I had a player once send out, "Does anyone know any dialect of elvish?" and boy howdy that was right in my character's little linguistics nerd wheelhouse, so I got fed a little more information. If you give them a chance to use this in a plot, they're probably going to be happy. I tend to look at players' rphooks, or wiki 'Interests' field, or whatever before finalizing a plot's details for that reason.
- Players do want to feel like they affect the world. Obviously, you can't really have a PRP let someone blow up a prominent building or assassinate the king or whatever, at least not without tapping the staff in at some point and going, "...help?" But if a PRP takes place entirely in its own little pocket, they will be sad. Give them something to take back, whether metaphorically or literally.
- To use Arx as an example again, the clue system is great for this, now that you can create PRP clues yourself. I've also let people find old objects—not artifacts of power, but things they can take home as a remembrance anyway.
- I've also tried to leave at least one hanging plot thread from each plot, so that players can pick it up and run with it themselves for more PRPs (or I can pick it up later). The demon-tainted shavs who got away during the Hunting the Beast plot, the one mural they couldn't decipher in Choose Wisely, the whole lingering question of "where the hells did he go after he did this" for the villain behind The Forgotten City, etc. Even if it doesn't affect the main metaplot, feeling like it wasn't just a self-contained one-off—as if it's part of the world, and there's still consequences and things to look into after they get home—seems to help player investment, and keeps it from feeling like it took place entirely in its own little pocket world.
- Thematic consistency is important. You might be GM'ing this PRP separately from Tony's PRP, and both of you are doing things entirely separate from Staffer Julie. But for the players, it's all the same world; people are going to take whatever you did and bring it back to mainline plot stuff. If I make a demon in my plot who can be defeated by one specific means—say, they cannot tolerate the presence of one specific plant—and the players defeat the demon that way, I guarantee you that the players are going to share that info around, and the one player from my PRP who is later on some other plot is going to want to try that plant against the next demon they face.
- Obviously, it's easier to run PRPs within a narrow thematic channel ("a skirmish with the Cylons", "Bringers in the city again") and fit it in to ongoing things neatly than it is the overall wider world and entire theme ("I'm gonna run a big plot involving Ha'la'tha smuggling!" "I'm gonna have you all face a Demon Knight who enslaved a village!"). Give players hooks to hang their PRPs off of where you'd like to encourage RP—carve those thematic channels for PRPs to flow through—and you'll see it happen. Witness, for instance, the sudden spate of "I'm gonna run a PRP!" during the siege on Arx.
If you can hit all those points, you can keep players engaged, and the PRPs feel like something that actually ties into and effects the world.
So I feel like one key is to facilitate that. Make a PRP GM interest group, a channel for players to trade GM tips and tricks; GMs love to chat about things they're planning, even just in the abstract. Make tools to help them; I know Arx is working on +goal and +prpgm systems, which should make it much easier to hit those points. I know FS3 games allow players to setup and run the combat code just like a staff GM would, which hugely facilitates things like players running skirmishes on BSGU. The more information they can get to plan PRPs, the better; the fact that @faraday posts the goals for a given 'campaign' helps players GM stuff that feels like it fits into that specific campaign.
And if you make it possible for PRPs to feel like a living, effective part of the world, I think you can keep the game fairly active even without staff having to kill themselves or end up run ragged trying to GM or oversee everything.
That's my overly-lengthy $0.02, anyway. 
