One of the more important effects of targeted abilities which is the reason I'm terrified that they'll skillshotify Ryze's Q (making it Ezreal's mystic shot sans on-hit stuff basically) is that units can't block them.
Usually anyway, but I don't know of a single target, point&click ability which can be blocked by interceding units, The closest you get as far as I know would be Lulu's passive.
So why is this a big deal? Because you can't farm with single target skillshots. You can snag opportunistic last hits, but you can't use abilities like Mystic Shot, Glitterlance, Light Binding, to farm.
Which is why I'm terrified about Ryze, because all he has to reliably help him farm is a targeted point&click single target spell, which Riot stated they think is an obvious candidate for being turned into a skillshot.
As for point&click CC
It's fine, it should pay for it's reliability in duration, strength, cooldowns, resource costs and range. The problem with stuff like Taric's stun, is that it has too much range for Taric's otherwise melee profile, and too long duration for something you can't avoid.
Then you have Ryze's root which is short range, and doesn't last very long at all.
It's more about what the ability is supposed to do, and more importantly what it does in play, than it is about what kind of ability it is.
And It's not like there aren't skillshots that are a lot more reliable than targeted abilities anyway, due to being AoE and having range a targeted ability couldn't afford.