There's really only one complaint I've heard about runes that I agree with, that being the sheer amount of RNG that goes into them.
PvE:
Run the Dungeons to buy/get the Rune: Face Runes, RNG
Run an entire Dungeon, just to find out if you got the materials or not, RNG
Upgrading the Runes: RNG on a soul crushing degree.
PvP:
Play PvP Til you buy the rune: Honor is RNG based on you winning, AND the RNG of the team you fight, ie Victory is a form of RNG in ROSE due to power disparities.
Amount of Materials per day, RNG, you never know how many wins you can get in a day during the 3 hours PvP is actually active, RNG.
Upgrading Rune, RNG in it's purest form.
There's only 1 factor to runes that isn't based on RNG, Daily Quest amounts. Should you power through the RNG of PvP or Yolo DG qeues, you'll at least be given a guaranteed amount.
The rest of the arguments?
I'm lazy
I don't want to
People with Runes are just dupers anyway
Dupers ruined Runes because they duped them, 'tainting' them and making them unworthy of my persuit.
etc etc
All excuses.
Fix the rune system, in a way that rewards effort, but isn't so heavily RNG, and the majority of complaints will stop. Not all obviously.