I think it is just part of the natural RNG of this game. There are probably different priorities that could be set that might make it better. Maybe always shoot skill shots towards the highest density, but then there is still the possibility that that average position line misses everything. I think the only skill shots that could be corrected better, would be the occasional one where someone is behind a champ and they turn around and shoot it at one person instead of at the whole team. But then if it didn't shoot behind and take out that one, you might have people complain that it should take out the most pressing threat because then it would continue to fight and maybe do more?
So should a unit target the immediate threat with a skill shot or the most damage overall? If it was vs a yordle team, I would want that dragon to blast their whole team, but if it was an SOS Pyke behind I'd rather it blast the solo target LOL. Also if there were different priorities for targets, than that just might open up other ways of gaming the skill shots. I do that when I vs a blitz. I put one tank like a Garen on the far side of the map from blitz and he pulls it right in instead of pulling my ADC.
I guess that it is possible to maybe tighten up the AI, but I think you will always have the possibility of just really off shots, but they aren't usually that bad. The only ones I get annoyed at is when someone burns their skill on a unit that is already in the process of dying while their Draven is pounding on you.