MTB hub with different size flanges?
You mean larger right side flange. Making the left side larger on a derailer wheel would exacerbate the tension disparity, not equalize it.

There are companies that do it. The reason it's not more common is that the difference has to be pretty radical (i.e. a way more expensive shell to produce) before the tension disparity is affected much, and at the same time, it doesn't take much difference at all before lacing the hub gets difficult using conventional j-bend spokes. 

On 6-bolt hubs, the left side already has to be around 58mm, so making the right side much larger means starting with just a really big piece of al, and I believe that's why it's seldom done.

The only tall left side mountain hub I know of is the DMR Revolver. I have no idea why they did it that way. But if you want equal spoke tensions, don't buy that hub.