As long as the instances are static, people will farm the one that is easiest and fastest.
A solution I proposed about a year ago involves some coding, but not a lot, on the part of Turbine. Essentially if an instance gets run a lot compared to others, it starts dropping less loot, marks, and medallions. Other, less frequently run instances start dropping more. Have limiters on it, say, 50% normal and 200% normal. Occasional human review to be sure things are not getting out of whack and revise what normal means on an occasional basis. Within a very short period of time, most instances will be run fairly equally.
I think this gets what the OP wants, which I think is more instance diversity.
Maybe someday Turbine can try this.
Viniel, 100 Minstrel -- Tokomak, 100 Guard -- Valwin, 100 Captain -- Vinlad, 100 Burglar -- Vinius, 100 Champion -- (and others)