The solution could be a global party search sort of thing - that's usable and persistent even when you not in town etc. To reduce spamming you only allow preset messages/items (missions, outposts, PvP) and limit the amount of stuff you can queue for (3?), and you group the items - so if there are 7 players queuing for "Fort Aspenwood (Luxon)" you'd just see one entry with the player count of 7 there, and the queuing players only get a popup when the required team sizes are met (both Kurz and Luxon). Options: would be nice if it gave you a list of the queuing player names if you clicked on the player count. Even better if you could select a toon for a particular queue, and play with a different toon but this would likely be too hard to implement!
The problem with stuff like HA and GvG is many players want a "perfect" team build. So how do you get the players together and then how do you do something fun while queuing the "perfect" team for the actual match? The first problem can probably be kind of solved with the better queue system but I don't see an easy to implement solution to the second problem. The workaround for players is to buy and use another GW1 account (implementing a purchasable sign-in as multiple toons option might be too hard at this point - so many problems e.g. where do the PM'ed messages go etc

For FA, AB, and JQ maybe dropping the minimum player requirement down to two (one per side) could help. If one side only has X players (where X is lower than the max) the other side will only have X players too - gives an incentive to talk to the suspicious/shady kurzick/luxon . Maybe have two buttons "enter full battle" (normal), "enter quick battle" (where smaller than full teams are allowed). Yes the 1v1 matches would be silly esp for FA, but less boring than standing around. And if enough silly 1 v 1 people turn up, you end up with more than 1 v 1.
p.s. could have the queuing be for PvE missions as well. Then you'd have a tree style sort of thing - PvP, PvE being top categories then for PvE - Prophecies, Factions, Nightfall, EoTN. when the tree or branch is collapsed you'll see the total number of queueing players in that collapsed branch.