I have played many similar genre games. So i am going to provide some ideas based off on my experience. 
1. Quests and Wiki -
              All the games of this genre that i have played earlier had their respective wikis.
                       And also a basic level quest is at least there to provide a short tutorial of game to players so that rather than reading they do it practically and learn fast. However I feel without a quest games are boring so we shouldn't just stop at that basic quest only, we should provide very long storylines quests which make game more interesting rather than plainly upgrading skills for no reason (or just for rankings). Infact those quests should be ever expanding, new quests generated in every update so fun never dies in your game.
2. Universal Buffs - 
              Games are not games if they are dead, less traffic/crowd. For this many games employ universal buffs system, where the paid members when donate provides universal buffs so that other non paying people took benefit from it as well, and thus keep f2p people happy as well, and thus game will not lack in crowd. In my previous game buffs were like - quindecuple exp, decuple exp, ez mode where no failures happen during any kind of profession/skills, unlimited stamina mode etc. etc. Also there are few pools for such buffs where whole community can donate too and when pool is filled universal buff is automatically activated.
3. Clans - 
            Biggest attraction is clans, its WIP in this game, i think Ryan should do his best to finish it asap.

        I don't wanna suggest all in one go so be patient once i see that my suggestions are being implemented i will bring up more  
Also i will suggest quests if i am asked for them

Continuation of my Ideas

4. Passive Gathering - In my old game apart from main farming, their was also option for passive gathering like some people want tin ore, copper ore for smelting to bronze bars, so main player farms for tin ore while his passive gathering mode is focused on tin ore. This mode is slow as compared to real player though, but its still fun having this feature.

Edit for Idea No. 3 - In clans the WIP buttons as shown in Guild HQs doesn't list an Guild Storage. You should be implementing that as well, so that high level players rather than selling their used items can provide them for use to their clanmates which are new and low level. Also they should be clan bound, like say if someone say X wants to take Y item and he leaves the guild then he should not be allowed to leave the guild unless he donate that item back to the guild storage.

Clan bank real importante imo. Auction house is nice but not for people in a guild. we like to create stuff for each other but can't even transfer atm.

Auto combat next enemy and auto heal at certain % of health with set food.