The game story and missions should be on rails while the actual content shouldn't be. The story they have down pretty much completely. Make some areas that are challenging to get through with a group (Like CoP and the aqueducts/riverne sites/etc) and I'll be happy story wise. Journal can take care of you if you get lost.

Leveling and exploring should be freeform. You should be able to group up with a small group of people and hunt a camp of monsters. You should be able to team up with a band of linkshell members and explore a cave (Sposhae) and level up while adventuring. And you should even be allowed to solo in a forest while looking for trees to chop down.

Quests should be done as they are now, but I wouldn't mind quest hubbish towns or NPCs. I'd rather you do quests for the material rewards than the EXP ones.

EXP should be the side factor: You level up as you have fun. It shouldn't be: You have fun when you level up.

End game should be also factor into the exploration. Having to find a HNMs inhabiting a pond in the middle of a forest or knowing that in a certain part of a zone when you see a sandstorm a Sandworm is ripe for the killing.

I don't mind direction, but let's be honest: The only direction you really need is for the quests/missions in your journal. Maybe some starting camps or locations to check out for new players, recipes for crafts, etc for people who are overwhelmed.