I had a whole year to think about these problems.
First up: Obilisk blocking and resource blocking.
In PvP, it’s fine…
In PvE, the solution would be the addition of brimstone veined rocknoses, and sustainable farming.
If players can secure their own economy, and make it geo-independant, then griefers can do all they want, it won’t affect the players much.
Considering the predominance of stone on a map, and their prevalence in pre-existing no-build zones, they make for reliable primary resources to fuel an economy: - Veined Rocknoses.
For wood, and plants of any kind, sustainable farming would be a solution, where one plant always returns 1 seed, but has a chance to drop an additional one. This could be a good source of wood and fiber.
One needs to show griefers that it is futile to grief, to fight this problem. Admittedly, these solutions only work if you are already established and a griefer arrives to wreak havoc. But if you are just starting out, you do have the luxury of just relocating to a different server without much relative loss.
On to the next problem. Overpowered weapons that were grandfathered.
So, you nerfed Crom-Blades stats and drop rates, and yet their modded versions remain unchanged at 125+ damage (however this could just be a graphical bug).
This effectively means that new people have to try twice as hard to get a version that’s worse, while other’s get to enjoy the old weapon-modded version unabated. The folks who did get it early earned this as early adopters, so all the power to them. But what of the majority?
One good way of rectifying this unfortunate exclusivity of opportunity is to offer another opportunity that makes the previous one obsolete.
Add a greatsword that is just as powerful as the un-nerfed crom blade, make it eat all stamina on swing again, but keep it as rare as it is now, but make it so the wielder recieves 1000% more PvP damage from other players: The Atlantean Sword of PvE Justice.