I think that expecting people to engage in this feature the way you think SE intended is even more unreasonable than expecting every group on top of a mark to wait forever for every straggler to get there. The way hunts are played is the way we as a majority group decided to play them. I'm sorry, I don't think that is going to change. I can see why people vent about it, but no one will suddenly decide that you are right and stop using the means available to them to get as many seals in as little time as possible. You could say the system is being exploited, but that's just MMOs for you! Players will generally opt for any way to mitigate the repetitive grind developers bake into their games and it's a little odd to blame players for it.

As for the Ninja thing, honestly, if you are part of multiple hunting LS' and an FC which all communicate fluidly, it's almost impossible not to know the location of the next A Rank mark within seconds of it being discovered. It takes a long time for a single group to kill an A-Rank, if they manage to at all. By then, chances are someone will have seen the fight and called it out. In the end, it still will not have a been a single party killing the mob, since there's no claim system.

General M.O. for large hunting groups: If you find an A Rank mark, you call out to your group with the coordinates. When the whole group is in the right zone and at a safe proximity to the mark, you shout out to the zone, your FC and all your hunting LS'. Then you consider how far you are from the nearest teleporter, add the 20 or so seconds it'll usually take for the message to spread to the masses, and simply call out a reasonable pull time. You don't have to rack you brain over it. Just the act of doing so sets people's expectations and eliminates a lot of eventual whining.

Occasionally, there will be players who pull marks as soon as they get to them, disrupting everything under some supposedly principled pretense that this is the way it should be done, and people are selfish for wanting to make them wait (I always find that backward logic disturbing). I found that it often has nothing to do with principles. It's always cowardly sad people who simply crave notoriety and like the idea of affecting so many other people negatively and especially, anonymously behind an avatar. They're usually easy to spot because a bunch of people are constantly complaining about them. When someone like that is around, you simply make sure they are not part of any of your hunting LS'or FC, and you stop using /shout until you don't see them around any more.

All that said, although this is a relatively fair and inclusive system that insures most people get good progress, it doesn't help people who are semi afk and not actively hunting - leeching, so to speak. It doesn't help people who don't bother joining hunting LS' or FCs. It doesn't help people who don't yet know all the maps and the best shortcuts to get to places (ex: Mark in Mid to Northern LLN? Use Upper Decks --> Tempest Gate). This means there will always be stragglers who may complain because they couldn't get to the mark in a reasonable time, while blaming it on early pulls. It is impossible to include and please every single person in a fight, but we can make an effort to include a reasonable amount of people. I don't see how that hurts anyone. The only exception I can see is if there are multiple A Rank marks up simultaneously and things may need to be rushed. That doesn't happen that much though.

To notify your party, target the mark and:
/p <t> sighted at <pos>

To notify your FC and LS', target the mark and:
/fc <t> sighted at <pos>
/l1 <t> sighted at <pos>
/l2 <t> sighted at <pos>
/l3 <t> sighted at <pos>

To transmit clickable coordinates to you party, which you have received from an LS, your FC or a shout: click on the coordinates to get the flag on your map and:
/p A Rank Mark sighted at <flag>

To everyone else:
/sh A Rank Mark sighted at <flag>
/fc A Rank Mark sighted at <flag>
/l1 A Rank Mark sighted at <flag>
/l2 A Rank Mark sighted at <flag>

It may not be what some people think hunting should be like, but it is still hunting. It is still "Search and kill". It just happens to be a large coordinated group effort. Getting frustrated and disruptive because you'd like it to be 8 people instead 60 won't make people any less pissed at you for pulling at an unreasonable time. So doing it that way is not fun or fulfilling for some of you and in your eyes, that may justify pulling whenever you want, but it seems that the majority of people seem to disagree. Perhaps most people find some fulfillment in progressing faster too. The kicker is that this isn't even a zero sum game! People still get their seals and yet still complain. If this vocal minority feels "oppressed" by this, all I can say is wow - First World Problems...