Something I learned when making games, ideas might sound good on paper, or might sound bad on paper but once you actually put it into a game you cant really know. There have been many times where I thought an idea sounded bad, and after trying it out it was pretty good and same with the opposite.

Don't make a huge list of ideas that you want to put into a single game and then try to make the game exactly how you envision it. Instead, take one of your ideas, and try it out in a simple prototype. Make the prototype quickly. Don't create any fancy graphics for it and use whatever tool is fastest to try out that one idea. Use Unity, RPG maker, the starcraft II map editor, or even prototype your ideas using physical objects if possible. See what is good about the idea, and what isn't. Then try to fix what is broken and take what is good and make it better.

By doing more small prototypes you begin to learn what is fun and what isn't. Then start combining your ideas in interesting ways. After you have had some time experimenting, then you can start to think how all of this fits into a larger game. But, when you start to craft your game, you need to identify what the core mechanic will be and capitalize on that. If the most enjoyable part of your game is out battling monsters, players will not want to spend most of their time trading and crafting for better weapon stats. I'm not saying you can't include some of those elements, you just need to make sure the game keeps a definitive focus. The side quests should add to the gameplay, not detract from it.

I say this out of experience. I used to think that all it took for a game to be fun is a world to play in and stuff to do. It turns out that there is a lot more to it then that. I know this may not be what you want to hear but hold on to your dreams, even if it may take longer to get there.

1. pve
2. pvp
3. wvw
4. crafting/work

May I suggest that you make a working prototype of each of these game modes/leveling options? While I agree that an MMO is quite the daunting task for a first project (practically but not theoretically impossible), you can certainly implement chunks of the gameplay and eventually combine those components into a working model.

Take number one "pve" as an example. You could certainly make a working prototype of your character and combat system. If at the end of the process you have some primitive shapes that can engage in combat, use equipment, and level up, you have a GIANT WIN! Sure, it won't look like your end goal, but that isn't the point. You can worry about art assets later -- concern yourself with making the underlying ruleset work for PvE.

Then take the next step. Implement a very simple PvP prototype using the above ruleset. Simple -- as in a one-on-one battle. There are many ways to do the networking depending on the tools you use, but the core idea is to build on the PvE prototype. Spend time making this work, "feel", and resolve how you envision. Don't worry about art!

I don't know what number three stands for.

But four... crafting! Follow a similar plan used in number one -- create a separate crafting prototype using what you learned previously. Iterate, iterate, iterate!

If you can make four simple prototypes that outline the four major game tasks you describe, you'll be miles ahead of most new game developers. You can then take what you learned and really have a chance on making a playable, enjoyable product. This will take many months, even years. It will be hard work with little glamor. But it will teach you more than you can imagine!

Best of luck.

So, first a little off-topic advices :
1. Formating. Making list is good and can help understanding, but one sentence by line?
2. Acronyme, not everyone know what you are talking about, either put a glossary at the top or don't use acronym.
3. Go straight to the point! Using a narrative form to tell a gameplay exemple from time to time is nice, but not everytime.

I will also assume that you are talking theoricaly and don't aim to actually make that game and just want to share some ideas you have. And so I will try to answer those the best I can.

Now, to the point. I will try to break down your mechanism. (the number doesn't correspond to yours, but follow your order)

1 . Work : I assume you go talk to a NPC and he give you money and experience in his working line once a day. What kind of work? Do you (the player) have anything to do? Does it force you to do nothing for the duration of the work? Is there a mini game?

The way you describe it I can't imagine it more than boring. Look at how the work works (lol -o-) in other game such as World Of Warcraft (of course), or Dofus and Wakfu, and nearly all other MMORPG out there.

2. Start your own business. I imagine that you can create a shop somewhere. And define what you want to produce and what are your prices? Else, what do you do when you start your own business? Is there not a risk that there is to many business open? Does all the shop will fit somewhere on the map?

Seems not really possible. (technicaly and not technicaly)

3. Rent a house. You have to pay 10 silver (the maximum amount you can earn by working) each day for keeping the house? The economy is quite harsh ^^. Sleep, ok I see, that's what trigger the buff. Eat, dring, bath? What does those do?

And you can farm.

4. Go PvE : Nothing new. There is 5 zones, and the last is shared. What prevent the player to go to other map than the shared one? If there is nothing, the shared doesn't mean anyhing, right?

Naval battle? The idea is cool, really, but do you realize all the work implied? Will the playe rbe able to build boat? To drive boats? Each player has a boat? Or there is only scripted boat who are like moving platform? Can boat fight each other? And so on on the technical questions.

Once again, it's a nice idea, I would love to be able to have naval battle in a MMORPG.

5. PvP : Nothing new. All the player are given the same equipment, you mean all the player who have not the required level (Terra has this system, which I understand allow low-level player to enjoy Pvp.)? If not, what the point in having experience and killing mob after mob to get equipment?

Joining quickly a game give less exp and money? Why?

6. Crafting: Nothing new.

7. Trading run : That's a good idea. I think you could make a game only on this idea.

8. Commander : Once again it's a quite nice idea, but many question. Is there a limit on the number of commander? Is there a risk of having to many commander? If there is to commander, all the startegical point will be set as objective and thus lose their interest. And there is also a lot of technical difficulties.

9. You kill boss to have better equipment. Ok.
10. Fight for your server? How?
12. You can have GvG deathmatch. Ok.
13. More blahblah
14. No offense, but it seems like a bunch of words that you find nice. There is no explaination on what are those class and what do they do, no mechanics.

A class does not determine your weapon or your role (and so your stats to assume these roles), so a class is just a name?

Cool knight? bad guy? best martial arts? android? barbaric? Seriously?