I would say that this is largely dependent on your server. Although I will say that Potion, will most likely never be best for gold.
Xmutes and flasks both use 1 Golden Lotus, as well as another agent for the recipe, so it all comes down to that other items cost. If the green gems on your server are very pricey and you dont have a steady supply, flasks would be better profit for you as you can get the herbs from the farm, and would have no cost to make them besides a bit of time everyday at the farm. Even if the green gems are cheaper though you need to take into account the prices of blue gems. If a blue quality red gem uncut sells for 75g, and a winters bite flask sells for 125g, I would argue that at the time Elixer mastery would be better. However if the prices are reversed then Xmute mastery is better.
The prices are what dictate what is best, as per server there can be differences in prices of gems/flasks/living steel. I stay as Elixer master and I net some good gold off it, making sure I spend aroudn 25 mins before the usual raid start times of guilds to repost and sell flasks, and in a half hour of just reposting I can make upwards of 30k (prices permitting).
Overall, just look at your servers economy. If the flasks are outselling gems, go that way, if the gems outsell flasks, go there.
I posted the first bar of living steel on my server's AH and it sold for 20k. I made a gob of gold off living steel and primal diamonds for the next 2 weeks. After that, eh, it was back to playing the AH.
But if you want to make a few hundred gold per day from alchemy you can probably do that easiest with transmute mastery.