With regards to the Factions Plugin, here's a few ideas/thoughts:
Alliance Features - All types of alliance would share the Ally Chat
Military Alliance - This would cause two factions who agree (both using /f Millally factionname) to be bound to a mutual war feature - that is, if another faction declares war on one of the two, the other automatically enemies the attacking faction. This would not force them to remain at war - but if you truce/neutral/ally/ext the faction it will give a warning and turn the Military Alliance into a Diplomatic Alliance.
Diplomatic Alliance - Current alliances would become this. They would not be obliged to go to war on behalf of other DipAllies, but would be more inclined to and would have access to the Ally chat.
Vassal Alliance - This would be when one faction becomes completely subordinate to another. The Vassal would have all the same faction relations as the Ruling faction, and would not be able to change faction relations. The Vassal faction would be able to decide it's own leader & officers, as well as change it's description, but would have a line in the /f f stating "Is Vassal of RulingFactionName". They would be able to claim within 10 chunks of the ruling faction, but the ruling faction would get a one-sided ability to edit the Vassal's terrain. The Ruling faction would also get full perm access to the Vassal faction, except for disbandment, promotions. claim, name, description, and titles.
War & Truce Features
War Tribute Auto - This would allow an attacking faction to name their terms in-game and have it so that accepting surrender would automatically run the demands through - or, if the demands can't be met, notify both sides of this so they can negotiate a change in demands. It would work as follows: /f enemy factionname tribute [Money, Relation Set, Kick Playername, Custom] with Custom being followed by a custom tribute (ex: /f enemy factionname tribute Custom Book about how awesome we are!). Upon surrender, the tribute demand would be automatically met by the losing faction - regardless of which side is surrendering. So if the attacker loses and surrenders THEY pay the demanded tribute, even becoming a Vassal of the winning faction.
Warscore - This would keep track of the kill-death ratio of every faction enemy pair. Vassals & Military Allied factions would all count as a single entity under Warscore. It would be accessed in-game by using /f warscore factionname, giving a list of all current enemies and a killcount in the form of ratio [10:3] with the red number being the enemy deaths and the green being allied deaths (only if they were killed by a player of the enemy faction listed). There would also be a percentage, gained by dividing the smaller number by the larger. A [10:3] ratio would show up as 70% for the warscore percentage, showing the enemy faction has 70% of a complete victory due to having killed 70% more players than the enemy. This would allow PvP factions to keep proper track of their current wars and progress in said wars. It would probably be laggy though.
Surrender Truce Timer - This would make it so that when a faction surrenders to an enemy faction the enemy faction cannot enemy them until the timer runs out. The faction that surrendered also cannot enemy the winning faction for that duration. The duration should be editable based on the server, and should have a toggle for hardcore PvP servers that don't want to have forced surrenders. The surrender command would be /f surrender enemyfactionname. The enemy faction would have the choice of accepting or declining with /f surrender decline/accept factionname. There could also be a toggle-able "Autotruce" feature that forces a truce between factions when the Warscore reaches 1000% in favor of either faction - with the demanded tribute being taken out.
And that's what I've got for ideas on the faction plugin being altered/expanded. And naturally other features would be more important, like rebalancing PvP Traits & reworking armor durability and such. And of course all of the above suggestions would be limited by the rules of each individual server.