I'm creating a new thread for this topic since they changed the cost of various rune upgrades. The main changes were they reduced the cost to upgrade all runes (except Superior) and they also eliminated the need for celestial essence in Lesser and Improved runes. In my original post a few months ago, I was puzzled why they would have the same upgrade cost for Superior as they did for Lesser runes, so I'm glad they finally changed this.
The value-to-cost ratios were way out of whack previously and now they are much better. There is still, I think, a need to reduce the cost for higher star runes, as the cost currently doubles for each additional star on your rune, with the exception of going from 4 to 5 stars, where the cost increase is only 25% rather than 100%. Also, the jump in cost from rare to Heroic/Legendary is much too great I think. You can see the impact of this in the right side of the first chart below. For example, a Superior 2 Star Rare rune gives you an Attack rating of 244 for a cost of 80,940 gold. Compare this to a Greater 5 Star Rare rune which gives you an Attack rating of 244 for a cost of 242,820 gold. In this case the Superior rune costs 1/3 the gold of the Greater rune for the same Attack value. This is because of the doubling impact of increasing stars. If the increased stars actually had a greater impact on the value of the rune, it might make sense. However, star increases only very marginally increase the stat values, but at a very high cost.
In another example, compare a Superior Rare 5 star rune with an Improved Heroic 4 star rune. You get 283 Attack value from the Superior rune for a cost of 404,700. You only get 281 Attack value from the Improved rune for a cost of 1,131,000. So again, you are having to pay almost triple the cost for the Improved Heroic, and getting less value. This is because the cost jump from Rare to Heroic (and Legendary) is too large for the value you receive.
The right column of the first chart below, when sorted by descending Attack value is placing the highest value runes from top to bottom. The gold cost should follow this same pattern, with the highest value runes costing the most gold. To better match value to cost, they should consider reducing the upgrade cost for increasing stars and also reduce the cost jump going from rare to heroic/legendary.