Why don't they just balance the power of Weakness? That sounds like the real problem the game has. Maybe 1.5% damage rounded up? Or make it a bit more variable, that way you can make the most powerful cards have crippling weaknesses, while less busted cards aren't as bothered.
They already did that, In the Diamond and Pearl era of the TCG they were like that, regular cards had +20 or +30 weaknesses, while some lvl X cards had x2. I didn't actually play during that time, but almost every player I've seen that did, talks about that era as one of the best, if not the best in the game's history, so it can be done.