Would Sona with a skill shot be better or worse?
I would argue that If you change Sona's Q from auto target to a skillshot, she would see a small dip in win rate; then a massive spike due to being "WAY TO FUCKING POWERFUL". This might get a little long so bare with me. As it stands some people dislike how much damage Sona can output due to her auto target bolts followed up by right clicking. It takes no skill, she is just a button mash champion, "free damage", etc... So lets assume for a moment that Riot takes this to heart and removes the auto target aspect of Sona's Q, and replaces it with a skill shot. If we assuming nothing else about Sona's kit changes, how does this change effect Sona? If Q no longer auto targets, it would either need to be a single hit effect or an AOE.
If single target; the ability can now miss, it also can hit a minion and thus negate the desired effect. So now the ability can only hit one target, that means it's base damage would need to go up. The ability can wiff or not hit the target you were aiming for, this means more base damage to compensate for skill requirement. For argument lets say the base spell now does 70 magic damage at rank 1 and gets +25% scaling (a 50% bonus over current, to compensate for single target instead of double target). Each rank adds 45 damage (75% of what it currently does) so at rank 5 the spell if it hits now does 250 damage with 75% scaling. The rest of her kit still works the same way, so you still have to deal with auto attack, into Q, auto attack with powercord and empowered auto. So Sona now has a mildly harder time landing her damage BUT if she does you take a good amount more damage. Also keep in mind that these numbers may well be low considering you have a champion like Soraka who's primary damage output is almost equal to the purposed Sona damage, but Soraka's is an AOE.
If we assume instead that Sona's Q is now a skillshot that does an AOE, think something like
but maybe smaller and without the added effects. The ability can still miss if you fail to hit a target, but due to it's AOE nature damage would likely not be increased since it can hit multiple targets per cast. This sounds lovely until you notice that this change would mean that Sona is now a semi viable champion for clearing minion waves. This change also doesn't promise that Sona won't still burst you with AA + Q + empowered AA + powercord in .1 seconds.
So what is the idea choice between the two? Do you want Sona to have a harder time hitting you but do a lot more damage when she does? or would you prefer a Sona that can wave clear / hit you when you stand right behind your minions?