Here's some ideas on how to make PvP more fun and balance (weaken) Runes in PvP while not ruining them for PvE.
Increase Battle Ready's Health buff from 40% to 200%. This would prevent heroes from wiping out your entire team on the first turn, and make raids and PvP battles in general more strategy based, and less punishing for players who want to try off-meta heroes and new and unique combos. Currently fast heroes who do lots of damage are the meta, because their only use is doing lots of damage quickly. With a larger health buff, this won't really be as effective, making players consider heroes who have better long-term use and who excel in staying in battle longer, like Yasmin, Julius, Lilly, and most importantly... The goblin team! Yaaay!
Add a new passive to PvP for heroes called, "Rune Weakness". Rune Weakness would halve the stats on ALL runes! You have a rune that grants +600 attack in total? Now it would only grant 300! Runes that grant 10% damage reduction? Now only 5%! Got a rune for 15% damage vs Tanks? Now it's 7.5%! Everything would be cut in half! This would not only keep your runes un-touched for PvE, but make them much less effective in PvP. While strong runes would still grant significant bonuses, this change, combined with increasing the health buff, would further push players away from simple Shade/MK/Ponti/Emily combos and more towards unique, diverse teams that would be more fun to face, and still provide a challenge, yet not anything impossible. I think this change would be significant in making MK less of a staple of PvP defense teams, while not totally making him useless. After all, his durability combined with his high damage will allow him to stay useful no matter what the dev team throws at him.
Feel free to suggest other changes or your thoughts on these ideas! I'm confident the dev team does look over and consider forum posts for feedback, even if they don't always tell us they're watching, so every little bit helps.
Favorite hero: Indigo
Currently: Trying to get as many runes done as possible. Takes a lot of money, man!