Changes I would make that may or may not be popular. Read at your own risk.
All buffs last until you die or log out. Running to the ship every hour is needless busywork. Also adds a nice sort of "walk of shame" back to the ship when you die. I find that humorous. There should be non-buff related reasons to be on the ship such as crafting altars, auction and bank. Make it a hub for social activities instead of a 1 minute bounce every hour. More "social" amenities should be added to enforce this.
Resist buffs changed to % absorption instead of flat numbers. This keeps them relevant at all levels of play and perhaps even too good at high levels. The exact % would have to be looked at, but maybe 5/10/15 fully stacking off the top of my head.
Since guild slots are soon to be a grandfathered thing of the past, add shrines that replicate the bonuses. Add 4 tiers of hp and sp shrines that mimic the old guild bonuses so all players have access, though to a potentially lesser extent for those using the shrines.
Add "combination" shrines to fill in some gaps in rewards for higher guild levels. A single shrine that combines str/dex/con and one that combines wis/cha/int mean possibly fewer stops on the ship and adds more "virtual" amenity slots to add new things such as the guild sp/hp shrines listed above.