Now, I agree that her clear time isn't optimal and that she can be counterjungled quite easily, I don't think her damage output is as bad as everyone says it is. She is my favorite champion and I've definitely played her more than any other in the game.
If you recall, after her rework, her damage actually got a slight nerf, and while part of me was sad that it happened, I can totally see why. It was not uncommon for me to actually have the most kills and most damage by games end, before her nerf. I was absolutely steamrolling if I could get even a tiny lead.
I wouldn't disagree that her AP needs better scaling, but that's so as to give her more customization in her build paths. To be honest, I build very, very little AP when I play her and I can still do pretty good damage come mid-late game. Putting an Icebourne Gauntlet helps her damage immensely, and it also helps her mana problems.
So many people think of her as a pure health tank, but that's actually a bad way to build her. The only real health item that I usually put on her is a Sunfire Cape. Besides that, Spirit Visage is the next largest health addition. Since BOTRK is so popular right now, putting any more health on her is just asking to die quickly.
If they buffed her cooldowns or mana pool/regen, then her damage would actually end up being nerfed. Her "Q" at max rank will do more than 12% of their max health... That's why her "Q" is so damn expensive.
If you build her health/AP then even her "W" will be able to do some serious damage. That's not even counting whether you have a Sheen Proc on it.
Once again, I agree that her clear time and how easily she can be counterjungled is a bit of an issue, but her damage (vs. Champs anyway) isn't that bad. You just need to know how to build her.