This game has always devolved into "offline base raiding".
I've said this at least a few dozen times before over the past few years, but the whole raiding structure of the game needs revamping.
I've always suggested following the old MMO Shadowbanes tree and siege system. Something easily adopted into the game.
Make it so trees give invulnerability to a single building (and themselves) per level. To destroy a tree an item, a bane stone in Shadowbane, would be created at great cost and applied to the target guild. The target guild (defenders) would get to set the bane time,and have to defend their base during that window or destroy the bane stone. To help facilitate the destruction of the base or the defense, siege weapons where implemented. Both handheld and emplacements (trebuchets and catapults). They had high cost and did little to no damage vs people, but would be able to take out walls and other structures. Generally speaking a "quick" bane in Shadowbane took hours of grinding down walls and the tree. Walls always where open to damage and never could be protected, it wasn't unheard of to set emplacements and had them fire days in advance to weaken walls.
Not that TOL needs that level of preparation, but there where glorious fights of hundreds of people in that game. Many of the fights I took part in where 50-100 in my nation with 200-400 people in multiple other nations. 600+ people where not unheard of at banes as they often rilled up the entire server. Though that is where Shadowbane excelled and also failed, since the game used TCP lag and rubberbanding was horrible. 3+ minute constant lag spikes where normal server wide during active banes.
Shadowbane also had a great nation/guild system. There was a hierarchy of Nation and guilds. A nation owned a city (or more than one) and could have subservient guilds under them. Albion online implemented something taken from shadowbane that allowed guilds to form alliances. So instead of fixed factions you had emergent ones. Though to be honest free form factions would probably devolve into a single giant faction so I fully support the current locked faction system. I do wish we could form alliances within the factions still, with an option for faction members to have some access to allies bases and restricted access to storage.
BTW, Shadowbane folded in 2009, but there are a few emulation projects to this day, if anyone ever wants to get into it look me up on steam.
p.s.. Still offering free upgrade services on the NA server for carpentry if anyone needs walls/towers.