I've seen some ideas floating around about possibly including a Hunter's Guild or "Marks system" of some sort, like the one in Final Fantasy XII, so I decided to write out some ideas about how it might work. This is just speculation and brainstorming on my part, so feel free to discuss it and share your own ideas, and criticize or praise mine as you see fit.
New Trade skill Hunter's Guild - Designed at its core to be very much like the other trade skills, with levels that raise by performing guild related tasks, and being able to do better guild related things at higher levels, but focused on hunting monsters rather than crafting/fishing/mining type things. Basically, it would work like the system in FFXII, where you commission a hunt by checking a notice board in a pub, accepting the hunt, finding the NPC who posted the hunt on the board, confirming quest details, then finding and defeating the enemy, then returning to the NPC for your reward. But it would be modified somewhat to work well with a MMO environment.
1. Find the Guild Hall (perhaps have one in every town instead of only in a certain town for easier access; could make it a story related thing to add to the depth like it did in FFXII; like the governments of the world support it as a way to keep Notorious Monsters and the like under control since they can be a threat to people, and alleviate the stress of having to spend government money and taxes to send soldiers, so they supported the forming of the guild as a separate independent organization in the world, kind of like the Tenshodo in FFXI, to allow adventurers privileges to hunt them instead) and talk to the Guild Master NPC to join.
2. Once you are in, go find a notice board in a pub or public place. Unlike in FFXII, perhaps the notice boards would not have the same marks on each one, to encourage people to explore the other towns, and it would also make sense, one mark might not really affect people in another town as much, and the locals would only post it locally. But there could be really bad marks that either a particularly desperate client wanted gone so bad that he posted it on every notice board he could find, or that affect all the towns, or maybe the governments are having trouble and they posted a request themselves, that can be found on most/any notice board.
3. Find an NM that you want to kill. Information would be sketchy. Level of the NM and difficulty, etc., would not be shown. You'd have to use your own judgment. Maybe some subtle hints could be given in the NPC's request, and perhaps more when you talk to the NPC in person, but nothing would be known for certain, you'd have to see for yourself. However, depending on your level (or "progress") some NMs may not appear on the list for you. Or maybe they appear, but the client will turn you down, not believing you can handle it, until you get to a greater level of advancement.
4. Once the client accepts you, details known by the client will be given to you. "I was attacked in this area at this location" or "I saw it near -insert area related landmark here like a waterfall or something-" "but it seems to appear only in rainy weather" or something similar to this. In other words, some would be already waiting at a designated spot where it likes to prowl, others would be hidden and require special conditions to be met before it appears. Could be anything, the weather, other monsters present/not present, killing monsters of the same family as the mark, not killing monsters of the same family as the mark, the mark fears a certain other creature so you have to kill all of those that are nearby, and so on, the possibilities are endless. However, the marks should not appear unless you have the quest for hunting it flagged with the appropriate NPC. And if more people are hunting it, it will have a low respawn timer so eventually you will get your chance.
5. Once the Mark has been found, the battle begins.. or maybe not. Perhaps while some are ready to rumble right away, others might have to be chased down. Or perhaps getting it to appear doesn't matter unless it likes you, or something you have. Maybe an item is needed to make it appear in Step 4 above, or perhaps that item isn't needed to get it to appear, but to get it to stay put. Basically, adding an element of strategy to it beyond just mere combat strategy. And while many marks could be potentially soloed, there would be certain ones that would need a group. Imagine a chocobo NM for example, that runs really fast, and you have to basically get it cornered. One person could not possibly run that fast or head it off, but a group, working together, could corner it. Then maybe, you need to put some greens down to make it stay put, so you can begin to fight it. As long as the greens are in effect, it would stay and fight. But when the greens wear, you either have to drop some more before the previous greens fade or you'll have to repeat the chase. Just a basic example, there is considerable room for many many more possible mark types and strategies, and if this was implemented, more marks could be designed and added in future updates.
6. After defeating the mark, you return to the NPC. Perhaps a key item or one rare/ex item for every member who assisted is dropped upon its defeat. Then, everyone returns to the questgiver and turns in the item. The questgiver gives a reward (an item of some sort, the harder the mark the better the item) and you are rewarded some gil and exp in addition to the exp you obtained when you defeated the mark.
7. Defeating marks earns you guild points. These guild points can be used to purchase special gear and items available only at the guild. Being a hunter's guild, most of these items could be nice rare/ex equipment for various jobs to use. Perhaps you could buy other things though, like an enhancement to your map that places a marker where the mark(s) you have flagged are said to spawn, or some other utilities to help you in your hunts. After gaining so many points you rank up in the guild, and can take on harder marks. In addition, as your fame in the guild increases with rank up, sometimes the guild will ask you to hunt a special mark that can't be found on the notice board. These marks would be far harder than the 'normal marks' on the notice board, but would give very nice EXP, money, and guild points when defeated. And the guild would reward you with a fittingly nice reward based on the difficulty of the mark. The rewards for these special marks would be generally far nicer than most of the notice board marks. As your character's personal level/growth/whatever it is rises, and as your guild rank rises, so too does your fame in the hunters world. Sometimes, an NPC might approach you, or some NPCs might say different things to you, asking you to hunt a mark that isn't posted, opening special "Independent Hunts" that sort of fall outside the Guild's jurisdiction. These would be special rare hunts that give the usual EXP, item and money rewards, and in addition, would earn you a great deal more guild points than normal, because you introduced a new monster to the guild that it wasn't aware of. This would earn you special fame in the guild and could even be a springboard to yet more hunts in the future. Certain marks could give you perhaps a new title too, if there is going to be titles again.
8. Marks are repeatable. That way, you can relive some of the best marks, and also repeating marks will make it easier to earn guild points towards the item you want and to the next rank up.