You summed this up pretty well.
The two things I really hate about Vayne and always have is that there's no effective counterbuild to her damage (I know Randuin's Omen and Frozen Heart slow attack speed, but that's small comfort in the face of a Vayne) and her playerbase tends to be unbearable behavior-wise.
I wish they would at least change the true damage to just magic or physical damage so there would at least be a theoretical counter (though magic damage might open up the risk of giving her mage builds, which I don't think we want).
Also, I think there's a problem with her being both a marksman and an assassin. Some clearing up of her role and play pattern would be good too. Maybe frontloading her damage somehow instead of having extremely high DPS? I think a pattern of burst>dodge>chase>repeat would suit her better than constant chasing and being simultaneously slippery and sticky. Giving her a small moment of weakness when she attacks would also be a fun counterplay.
Maybe instead of having a 3-stack mechanic, she could have a targeting mechanic like Quinn's passive that rewards her for choosing someone to burst damage on instead of incentivizing staying on someone for a long time. It would also telegraph her attacks and open up space for counterplay like Riot likes to do nowadays.
I feel like a reworked Vayne like this would have a lot of potential to be a fun and satisfying champion, but a she is and was for a long time she's really annoying for both teams.