After reading the following regarding Alchemy...
I wouldn't be surprised if you had new alchemy stones in a coming patch and you will have epic transmutations for 4.3 so they will have some big updates for you guys.
Source: http://www.wowheadnews.com/blog=1908...4-2-craftables
I'm guessing epic gems will be available in 4.3 whenever that might be. The comment doesn't suggest if the gems will come from current ore or something new.. but at least we know WHEN to expect em...