Sorry, if something was already suggested, but just i summarize what i would see in game:
1. Complete Encyclopedia Rites, to cover the History amd Knowledge of Atys with nice quests. The quests should have an increasing difficulty, with the final rite involving something hard. These quests should be shared by the entire team. The page filled in the Encyclopedia would be granted to whole team, while the rewards only to team members that met the requirements (fame).
2. Make 'tweaking' possible as this is one of the things that always have a big success in most of MMO. Tweaking examples: Some buff (as flowers) gives you the ability to wear/use better stuff, till u unwear for some reason. You should have accomplished a specific rite to be able to use the flowers. Flowers should be ecosystem dependant and only some special kind (rare) can give the tweaking buff. Introduce new crafting line for tweaked lvl 250 homins, that can produce higher stuff.
3. Make Tribes more important. Actually the only importance of raising tribe fame is to use safety their camp. Add some new behaviour: a guild with an overall very negative fame can have OP attacked by the enemy tribe (this is a PvE situation). The tribe can, randomly decide to attack the OP even if there is a PvP war established (this add some random odds to the PvP war). Also, put some special quest for friendly tribes that can give a special reward.
4. Add buyable storage to put into apartment/gh. Containers should have the renaming options. Special containers should be used for jewels, so you can group and name a set, and trade the whole set at once. Same can be done for armors.
5. Remove the way actually drills produce OP stuff and put them automatically in GH (more later).
6. New kami/karavan npc can give special quests to gain honor points. (see point 12 if u are neutral)
7. Make bosses randomly appears at different places in their region. With a knowledgeable random values: ie: "kirokya have a chance to spawn after 1 day=5% 2 days=20%". Make special actions in region that can 'trigger' the appearance of the boss (ie: it can increase the chance to spawn, just to say, from 75% to 100% depending on the actions).
8. Make "Spires" without affecting non-tagged players (no changes in the PvE aspect of the game). The actual timer to untag (and use tp's) is enough to prevent the abuse of the untag system. Eventually, every bonus/buff related to the towers would apply to tagged players only (incentive for a full PvP environment, without wasting gameplay to PvE lovers).
9. Make OP battles without the timer(the flag, not the start of war). Entering/exiting the contested area, instantly change your flag. In this way we solve the camping problems, new strategies can be involved with such behaviour (had experience in AO-Notum Wars and i can say this can work well). NPC guards will not be attackable outside of the contested area (the pvp area). Remove the 'neutral option' in the side-choice window. if you don't want to be involved into the war, just stay away.
10. New buildings at the Outposts: a stable that can feed animals sold by the guild. The guild decide the price (depending on the region the op is) and earn the dappers. The service would be free of charge for members, of course. A guarding tower that can prevent aggro mobs, so we can solve the aggro dragging behaviour. In this scenario, aggro dragging became an accepted tactic, so to incentive guilds to build the tower. A special building that, with a constant 'charge' of something (to decide what) can give the guild some specific dig spot near the OP. This should involve dappers, special stuff to insert in the building and production time.
11. Personal merchants and auction house. Nothing more to say. this should involve specific costs.
12. It's time that trykers learn how to surf with boats.
13. Outposts in PR. With special new mats. In a previous post i suggested the use of caravans composed by 1 or 2 cars with these rules: look here
http://forums.ryzom.com/forum/showthread.php?t=30483&highlight=cars for more (and forget the mentioned 'goo' as seemed cathced a lot of complains, but the idea is about cars not the goo, that can be substituted with anything else).
14. Make neutrals a real faction, with specific npc for the faction quests (to get honor points). TP agreements with high powers can change during time with an evolving lore. Make neutrals taggable.
15. Make Ring useful, at least for social purpose. This can be the core for customizable apartment, customizable gh.
16. Add a new crafting line: social clothing! To craft something nice to wear but totally useless in combat (no stats, no requirements)
17. Make random events triggered in game, without human intervention (no event team involved). Special bubbles chat from npc in towns can advice about 'rumours' till something happens: an invasion, a kitin concentration in some point, a special kitin boss (rare) appears somewhere, etc... these can be easy hardcoded similar to the bosses spawning rules.
18. Some new stanzas, earnable only with a mastery (or at certain levels, ie when u get the title) (and a quest/rite of course): charming, to gain a social pet - summoning (we already got the title, right?), to summon temporarily a combat pet (this involve the development of a pet system, so i just put the idea, nothing more).
19. Some new behaviour in the AI system: let the mobs very low in hp try to escape instead of suicide. This should put more fun in seeing animals interacting each other.
20. A real event team that can move the lore forward, with the help of us poor homins
21. Give us a path to the Canopy! I'm sure there are some valuable and unknown mats there and probably some new nasty creature!! Also, i wish to take some screenshot of Atys from that point of view!!
22. Put back the sound frequency of the environment and simply change the 'kipee' sound to be less annoying (not just overall dumby lowered). Put back the 'feeling' of Atys!!
In general, all of things mentioned should be done with a new economy balance, with high costs when needed, upkeep costs, etc...
Quests, being them not necessary but wanted, in some case, would be appreciated by casual gamers, not changing the real sandbox nature of the game.
Caravans and eventually boats can put more life in the world (that's already awesome).
I'm sure i forgot something, but, anyway.... Let's dream!!
An exquisite innocent looking kind of instrument that one really has to know how to use 
That realy would make it all too easy. Being constantly aware of your surroundings is part of the fun while digging!!! 
