there should be a miniquest that grants you an ability and/or special attack with the dragonbane 2h sword or else an untradeable variant of elder rune 2h sword that you upgrade with smithing that gives you a dragonrend ability.
that way when rune dragons go into their flying (2nd) phase, you will be able to at least melee them for the whole fight. its just making a melee variant of the dragonbane bolts for xbows.
there would be a magic ability too but these could just be small miniquests or something in order to make it so you can fairly use magic and melee at rune dragons.