It seems people in guilds don't even use the guild instance system. 9/10 people I come across doing the FG and CG have guilds. Which has to be super annoying for those actual newcomers. Not to mention half the time people are farming 1 item for 4 or 5 alts so they can box. I think, there should be an alternative. Perhaps add another 10 items to that list, and only make us turn in an X amount of items. That way at the very least, we can decrease spawn size/waits and still have some supply and demand.
That's more of the peoples problem, not the system. There are instances put in to counter these, but the people have to use them. I find the system as is perfectly fine except for a few of the spawns: Hadden, and Lord Bergurgle. Reason being, they have a long spawn time, dont always drop it/placeholder, and are lore, so they are not desirable to be farmed.
Going through the lists quickly...
Greater lightstone:lots of mobs to drop it
dragoon dirk: low respawn time (10mins?)
shiny brass shield: again low respawn time, 10-12mins i believe.
dwarven work boots: low spawn time, not lore
adamantile band: multiple drops, in an instance zone
Polished granite tomahawk: 4 different spawns drop this i've heard, only seen 2 though, including High pass
mithril 2 hander: mob spawns every 11ish mins, in an instance
Executioner Axe: (dislike this spawn personally lol) in an instance
Flowing black silk sash: in an instance
short sword of ykesha: not lore, in an instance.
Silver chitin hand wraps: drop rate in insanely high
fighting baton: multiple spawns, low spawn time too i believe
knuckle duster: not lore, in an instance
staff of forbidden rites: multiple drops off of kill
fungus tunic: in an instance
looking at that, it looks pretty easy to obtain to me... but of course this doesnt include the 2 main problematic drops.
Thaumaturgist Robe: multiple drops, quick spawn time i think
Flowing Black robe: low spawn time, but has a locked door which can be annoying.
Robe of the Oracle: instance available
Shining Metallic Robe: instance available
Light Burlap Sack: instance available
Advisor Robe: low spawn time
A Glowing Blasck stone: not sure on spawn time here, but the mob is usually up so never had a problem lol
Jade Reaver: ugh, do i need to explain this one? lol
Fishbone Earring: loooong spawn time, and doesn't always drop the item = QQGolden Efreeti boots: i think this is only a 15 min spawn time, but it might be 30.. cant seem to recall, hes usually up for me
Ring of the Ancients: 10 or so spawn time with placeholders
Lord Bergurgle's Crown: 30min spawn time with placeholders 
Red Dragon Tooth: multiple drops
Mana Robe: multiple drops
So really it seems only those 2 are worth complaining about, so maybe an instance for both the zones would be worth it, although not an 100k instance, but maybe 50k, since thats the going rate of the items, and they are lore so people won't farm them unless boxing and most would be too lazy to do that anyways lol. So you end up just buying the item with the 50k and the required time to get the item to drop, doesn't sound so bad to me.
Sorry for the pretty much unnecessary lists, but thought it might also show those that might complain about other drops, that really they are pretty easy camps and which have instances that some might not know about (OOT)
