i think being allowed to replace any un-owned card with quanta seems fair. makes it weaker, most likely over-quantaed, but the deck still runs.
having to use relics = dead cards. nobody likes dead cards.
Over quanta'd doesn't automatically mean weaker. In some cases (Nymphs vs Denial, weapons vs heavy PC, SoSac vs many purifies, etc) Pillars will be significantly stronger than the card they would be replacing.
Replacing Marks with Pillars is fine in my book - they're always going to be slightly inferior, barring a very unusual situation involving Nymph Queen/Tears. This was the system used last War. But replacing other cards with Pillars isn't a good idea, in my opinion. I could see it easily leading to abuse.
Why will you build a weak deck to abuse it with a substitution rule to pack in quanta instead of a rare???
Why not building the better deck with unlimited quanta directly?
Don't get what you fear, afda. 8)
You are playing a deck with 3 Auburn Nymphs in it. You are also playing 6 Steel Golems. This deck is an optimal build against the range of decks you expect to play against.
As it turns out, you're unexpectedly matched up against Discord/Earthquake. It's a match up that the Auburn Nymphs are bad in. But that's okay - you can sub, and the Auburn Nymphs become Pillars for you. With the extra Pillars instead of the expensive Nymphs your deck is much more likely to win. Yay!
Admittedly this is an extreme case, but it does highlight the issues.