Here is the story I came up with for the game. It is just a brief synopsis, but tell me if it makes sense. And of course, any feedback or observations you might be able to add are well taken and useful, so please, let me know.

From a game design standpoint I think it would be more beneficial to get feedback on the differences between the classes -- what makes a Rune Sage mechanically different from a Monster Slayer or Spell Warrior? -- and the way this magic actually functions in game rather than the specifics of the story. I'm much more interested in what effects the player's alignment has on gameplay rather than the fact that players can align with the evil Cascaval.

I want to know how the spells look, how the spells are cast, how they impact the world, how they can be countered/mitigated, and who can use them. You are making a game about sorcerers, so I think creating a sorcery system that is thematic and fun is more important than the specific who's-its and what's-its of a detailed backstory.

Think of Call of Duty... I don't know much about the story, but I sure know the game mechanics of shooting things are well defined and developed, which supports any story about shooting things. (I'm not a CoD player, so this example may be off) Make a great magic system that any story that focuses on magic will work with.

As GoCatGo said, from a game design point of view the story is not really important. Knowing the context is good enough (who, what, where, when, why)

The rest would rather belong in the writing section of the forum :)

(I might as well give my opinion on the story. No offense, but it seems to be a boring Manichean story with a possible face-heel turn at the end. And using a bad guy who is a bad guy because he do bad thing is a trap you can easily fall (event though here I don't have all the story). I like the fact that you added centaurs and fairy as playable races, if correctly used it can bring some freshness to an overused fantasy setting. But it should be sufficient for non-heavily-driven game. If you just want a simple setting it should be enough.)

(First and a little off subject, and sorry for bringing this, but a little formating is always appreciated :) )

I have few more questions :

1 - Moral orientation : in what their orientation affect the game? Does that affect only the story? Does the people in school will give ou free stuf if your are good? Does it restrain the people you can add to your party?

2 - Five classes, can they be categorized like following :

Spell Warriors (DPS)
Monster Slayers (DPS)
Rune Sage (All around)
Beast Master (All around)
Plant Wrangler (All around)
Charms Master (Tank?)

Finally, most of your class have both offensive and defensive power and finally seems identical. Why should I choose the Spell Warrior over the Monster slayer? Is there only there skill set which is different? Does they have special mechanism?

The rune mage system would be most interesting (in my opinion) if the tablet will give him either offensive power and boost, or defensive power and boost, not both. With what you describe, the only point in switching tablet is to match the enemies' element, right? (fire vs water, etc...)

(Formatting would definitely help my understanding as well!)

I have two main suggestions:

1. Find an extensive guide for a game you enjoy or know well (Fable seems to be a favorite of yours). Study it to see how the actual game mechanics work. You seem stuck in thinking that game design is simply saying "You cast a spell and have the choice to be good or evil!" You need a large dose of spreadsheets and formulas to design an RPG. You are missing meat in this sandwich -- so far you've only got a topping or two and a recipe for sauce.
2. This opinion (like all opinions) is entire subjective, but... Good/Neutral/Evil morality systems are so BioWare 2003. They offer very little to pique my interest and I consider myself to be a very typical (if not jaded) gamer. It tends to default to an obvious Good vs. Bad path with no real story options beyond being Captain Nice or Kommisar Jerkface. Find a more meaningful way for in-game choices to have in-game consequences.

I encourage you to seek story advice in the appropriate places and to make hard choices on actual design and mechanics for your game here. I'd be happy to provide templates or examples to you if you would find them helpful.

So the old morality system is old news? Ah so it goes.

I do not really agree (but, it's also an opinion, so ^^') In term of morality choice maybe good versus evil is outdated (what is good for you may be bad for other) but instead maybe having a kind of faction-based morality. For exemple, if you do something to help the forest (you hippi!) then you will gain some point in the drudic circle, if you don't (you capitalist!) you will gain point in the Mecamage corporation. By progressing on one or the other "faction" will give you bonus, equipment, and may influence the story.

An other solution would be achievement bonus. If you choose to free the unicorn you will have a permanent bonus of +1 in magic, but if you choose to eat it, you will have a permanent bonus of +1 in Strength. And some NPC will respond differently depending on your achivement.

I have never had to deal with mechanics before, but anything you can offer would be most welcome if you have links, templates or whatever.

If you want document on game design there is the excellent book : http://artofgamedesign.com/book/
There is also a lot of topic on this forum where people ask how to start, and the answers are generaly quite good :)

A type of online game that often goes unmentioned is what is called a 'villiage game' -- a term mostly-inspired by the first few successful examples of what is, essentially, a small-scale MMO.

Now, any game -- single player offline or , multi/villiage/massively-online -- is a huge undertaking, but there are a number of these small-scale MMO 'villiage games' that have been successfully running for years. No one's getting fabulously wealthy from them, but they're making a living. Villiage games are typified by embracing their modest player base (typically between 1000-10000 active subscriptions, and a few hundred to a couple thousand online players), rather than designing for mass-market like WOW. Players appreciate the more-intimate setting and community, and the devs typically provide a framework for the universe but incorporate community feedback seriously -- in a lot of ways, you can think of it as a smaller, more democratic MMORPG. In return, the player base, although small, tends to be extremely loyal, and generally lacking in griefing or other misbehavior. Most of these games are simpler in nature than WOW, or what you seem to describe, though -- many are 2D even -- but you can't expect to pay for modern AAA content on the backs of only a few thousand subscriptions.

I have never had to deal with mechanics before, but anything you can offer would be most welcome if you have links, templates or whatever.

I, like many people here, would be happy to point you in the right direction. Take nothing I might suggest as a hard-and-fast law, though -- most of it is very much what works well for me and my projects. I'm constantly touting the virtues of Machinations:

http://www.jorisdormans.nl/machinations/

and this document outlining RPG design patterns:

http://www.autzones.com/din6000/textes/semaine13/Kirk%282005%29.pdf

The Art of Game Design (http://artofgamedesign.com/), as suggested by Navezof, is indeed a MUST. No delay, just read it.

Maybe adding the morality things is not a good idea,

I may have been too harsh on what you wrote -- it is certainly a fine idea, but the difference between it turning out ::blah:: or AWESOME! in-game is how you implement it. If your morality is just a scale with EVIL on the left an GOOD on the right, set by a series of binary choices, I believe you might be in blah range. Again, my opinion. But with some elbow grease you can turn it into something enjoyable that supports the story you are telling.

You're in the right place to learn this stuff. Kudos for taking the time to read critical feedback and following up on the information -- that's a great sign that you might bring this game across the finish line! I will share anything I know with you. The more specific the question, the more likely you'll get the help you need from this community.