The Main and undeniable problem is that Sona is super weak until late-mid or late game. She can poke a little bit, and that's it. She is the only Support that needs to be carried to late game because she does not really offer anything herself.
Once Sona has a lot AP, the heal/shield is actually useful, the speed boost is actually useful and the Q does serious damage.
But that does not justify the fact that the heal/shield is non-existent early game, her speed boost is the worst of any other movement skill in the game, and her only semi-useful skill is her Q.
Furthermore, all AP Supports should have a spamable hard CC (Nami bubble, Morg bind, Lulu polymorph, Zyra root).
Right now there is no justification for picking Sona unless you want your team to carry you to late game - and the meta has nothing to do with it. Sona is just plain weak early game.
I am honestly not sure how she went through a rework and is in that terrible state. When you do a rework and do it wrong you are supposed to go back and fix it. You don't say "ok I am done with the rework, even though it was a failure, but simply because its done in name only, we will never go back again and fix it". What is really frustrating is that other champions get multiple balancing changes until their are just right, but when they make changes to AP Supports (Lulu anyone?) they give it one try, and then move on even if it totally fails and destroys the Champion.