While i agree with your statement that vayne should be changed to make her less oppressive, outright removing her would be bad. Sure i hate %hp true dmg as much as the next guy, and i think whoever thought of that as a concept should be smacked upside the head, but there is a niche for these types of champs.
The other 2 massive examples that come to mind are varrus and kogmaw, varrus can cc and destroy your hp with his blight stacks, and if you let kog just sit there, your team evaporates. The only difference with vayne is the only thing keeping her oppressive is the invisibility, and how safe condemn is, if you ignore the tank shredding playstyle. Have you ever caught a vayne toplane as darius or any other meele top? Without condemn, her q is a mediocre escape (not in ult, mind you) and she is easy pickings, since she needs to get into lucian range to deal damage (for the most part).
If i had to change her, id either turn her %hp true dmg into magic dmg, or increase condemns cooldown, stop it from applying passive stacks, and make it only knock you in the direction she aims it at (I,E no shooting at you and flashing above you to defy physics and stun you into a wall from a bolt that would clearly knock you away instead of into it).