No, runes are not ok in any way. They were balanced for maybe Orange 0 and 1. A system where you have an ok rune one promotion and after the next one it's total trash must be reworked. Also a system that after a new hero is released you must rerune 4-5 heroes to be viable at all is beyond frustrating.
Right now the best you can do is use rune stats that can't show up on gear, because that will never be obsolete. If this starting energy meta is fixed you must still ignore all Hail runes and fuse them right away. Same goes for any minor rune with main stat Dodge or Accuracy. No matter how great it looks otherwise the top stat is almost like a 0 and the only reason to use such a rune is if it was already developed and it has a 20-25% damage subtype bonus.
Last promotion Hail at least helped poor Megataur with his 0 Accuracy. This promotion he got an item that's worth 55 whole Hail sets. I give it 2 more promotions until good stats like Magic Penetration will be considered as a poor choice because of how little it will give compared to gear.