The concept behind the cool down is on the Alchemist Stone itself, not the type of material produced. One Stone = 1 cool down. What we would like to see is reduced cool down time based on the transmute.

Transmuting an elemental item from one to another should be 1 hour.
Transmuting one ore to another should be 4 hours
Transmuting transmuting end-game items like frost lotus, primordial sauronite, etc should be 8-24 hours.

Personally I would like to see alchemy drive down prices of end game material to about %50 of what it currently is. My reasoning is that I believe the prices of a number of servers are outside the intended economy of WoW. A person who does 25 dailies every day for a month should not be considered poor by any means and telling them to "learn how to A.H." is just out of line when part of what you do is keeping them out.

By all means let the auction house be a means of income for the savvy economist, but don't let it set the bar for competitiveness in other aspects of the game.

By allowing Alchemists to transmute old-world materials en masse, you take away power from people who have specialized knowledge and skill in gathering those materials and auctioning them. Those materials would all drop in price, and leveling most of those dependent professions becomes trivial.

Making relevant transmutes for the latest level of content off-cooldown lets undergeared toons catch up to current raids. Taking lower-level transmutes off cooldown does little aside from putting more power specifically in the hands of alchemists, while also potentially hurting other people's livelihoods.