Your statement is misleading, as the power gain will be off "upgrade rune" as opposed to "new rune"
6 lv 5 rune gives three times as much stat as upgrading 6 lv 5s into lv 6s, and that's what people will actually get. It's still a nice amount since it affect all your chars, effectively an extra awakening or so on your entire team, but it's not as drastic as you make it sound.