Maybe a rework to her Silver Bolts:
PASSIVE: Silver Tipped Bolts: Vayne does 2%maxHP true bonus damage on autoattacks.
ACTIVE (No cost): Pure Silver Bolts:
Vayne switches her ammunition to a heavier round made of pure silver. When activated her next (2 + ability rank) autoattacks deal 7% maxHP bonus true damage although at the cost of attack range (due to heavier projectiles). No attack range penalty during Final Hour (because she switches to a full-size crossbow). Passive component is lost while ability is cooling down similar to Wuju style. Lengthy cooldown to prevent abuse early game but cooldown reduces with autoattacks so she is still encouraged to build attack speed.
Not perfect by any means, but gets rid of the 3-hit nuke everyone hates. Let's her keep her trademark sustained %HP true damage with the passive component, gives her a "window of power" if she wants to quickly deal massive uncounterable damage and makes her more bursty but more predictable, and leaves her vulnerable once it's on cooldown. Makes her a bit more fair to fight against for immobile melees because she loses some of her range advantage if she boosts her %HP true dmg, but if she really wants to win the 1v1 she can keep her range advantage at the cost of her ultimate. Preferably also a rework to her condemn that turns it into a skillshot that hits the first champion or large monster so you can actually outplay it, but increases the cast range and kickback and possibly allows her to impale multiple enemies to a wall.
Then again it might not solve anything. It's a nightmare to balance %HP true damage on a ranged champion with two peels and stealth, they might have to start from square one.