The things we most want to avoid are:
1. Players being unable to defeat the PQ.
2. The PQ being trivial.
3. Players feeling like their contribution to defeating the PQ is meaningless.
4. Players feeling like it doesn't even matter if they complete the PQ or not.
If, for example, you have a particular zone be attacked by a group of 20 ogres then we can probably assume that 20 players can defeat the challenge. The trouble is that if there happen to be 50 players on hand then the ogres get mauled and put up no resistance so the event isn't going to be particularly challenging, interesting or memorable. If there are 5 players on hand they probably have no hope of victory so the PQ needs to be avoided or ignored instead; neither of those options are much good from anyone's perspective. Of course you can scale the difficulty based on who is involved so that the encounter is challenging for the group but that is both very challenging to do correctly and likely to make the players not care about it - why would I go help fight the ogres if it only makes them stronger? If 1 player alone can beat them what is the point in me helping out and won't I get yelled at if I am not a good player and end up being a drag on the team? If we scale the ogre attackers such that they are more powerful for each player in the zone then presumably it would require a large percentage of the players to work together to defeat the challenge. Everyone's contribution is still meaningful but in theory the encounter can be beaten no matter how populated the zone is. This does mean that anyone just idling in the zone who doesn't contribute to doing the PQ is making it harder on everyone else; I don't know that this is actually a problem but it is there.
I think the plan of scaling the PQ difficulty based on the population of players in the zone at the time is a good start. This way if people can recruit a lot of the zone to help or bring in outside assistance they can defeat the challenge and feel like everything they do matters. Unless the entire zone decides to go smash the PQ together it should present some reasonable difficulty and getting all players to do the same thing at once is not generally possible. The real trick is figuring out how hard to make the PQ - do you tune it for 50% of the zone, 80% of the zone or 20% of the zone showing up to help fight? If you guess too high then players will get the impression that the PQs are generally unbeatable and won't bother at all and if you guess too low then the players will get the impression that PQs are trivial and swarm them. One way to combat this would be to scale the rewards based on the zone population also; this would mean that people looking for a challenge and a big payoff would be more likely to try to try to do PQs if they were hard and players would be less inclined to join a massive zerg because their rewards would be diluted.
One thing that would drastically improve PQs would be to flatten the character improvement curve. If a PQ in WOW worked like my idea above then a max level character could just fly around easily defeating every PQ by themselves in seconds even though it might take 20 minutes for an entire zoneful of level 20s. For the system to make sense it would be important to have the most powerful characters be not as much better than the low level characters. One other very useful thing to have would be an interface element that allows people who want to group up for the event to do so easily. WOW doesn't currently have this but other games do; it isn't hard to implement.
A Sky-style PQ:
RNG decides to start a PQ in the Canyon of Terror!
There are 24 characters in the zone so 12 ogres spawn at the ogre cave and an outpost spawns a good distance from them.
A shout goes out across the zone that the ogres have come and will be destroying an outpost soon.
5 minutes later the ogres begin to walk across the zone towards the outpost.
10 minutes later the ogres reach the outpost and start fighting the guards (who are hopelessly outclassed).
5 minutes later the ogres destroy the outpost.
If at any point the ogres are defeated then any players who attacked them can talk to the boss at the outpost and get a reward based on Number of players in zone / Number of players who contributed. The outpost is available until the next ogre attack.
The idea is to make the PQ relevant (the outpost has quests, vendors or other uses), challenging but beatable (difficulty scales on number of people around who can participate), and every character can feel like their contribution and abilities mattered. Note that just spawning more and more enemies for the players to fight eventually leads to problems - better scaling mechanisms like increasing the damage and HP of the ogres would be necessary.