More spells should be targeted, and then tuned around being targeted, rather than being skillshots.

I know what you're thinking...

"But muh counterplay!"

Well, shut it. Making everything a skillshot is not a great way to introduce counterplay.

Making something a skillshot is, technically speaking, a downgrade. Because of this, these spells are always compensated in other areas.

• Some skillshots will have more damage than a targeted equivalent (Sej R can do 700 (+160% AP) plus a potential 200 (+60% AP) from her E proc, while Liss R does 350 (+60% AP) magic damage).
• Some skillshots will have more range than a targeted equivalent (Ryze's old Q had 625 range, the new one has 1000).
• Some skillshots will have lower CD's (Fiora's old Q had an unconditional 8 second CD after your second cast, the new one only has an 8 second CD if you miss).
• Some skillshots are allowed to exist in otherwise powerful kits, while targeted ones eat up a champion's power budget (Rakan's W is just one of the things he does, while Alistar's W-Q combo is most of his power budget).

Hell, there are even some situations where making a spell a skillshot is just a straight buff. Making Fiora's lunge a skillshot gave Fiora, a champions who previously had no escape, an escape.

What's worse is that Riot has a habit of taking an unhealthy champion, making something on them into a skillshot and saying "Boom, healthy".

Old Ryze's problem was that he had overwhelming damage on no CD alongside solid mobility and dumb levels of durability because he could buy ROA, Frozen Heart, and Banshees (which used to give Mana). New Ryze has less raw durability, but can now spam shields on himself (achieving basically the same effect), plus he does more damage than he used to (though he takes longer to get there). So neither of his real problems were addressed, and he's been made virtually unplayable for 99% of the playerbase.

Not only did you not fix the problem, you made it worse and then just made him unplayable for anybody below challenger so nobody would notice.

What if we made Rune Prison a skillshot, and then compensated by shaving 2 seconds off the CD, adding 350 cast range, and adding 50 damage? Would that make Ryze healthy? Absolutely fucking not.

On top of all that, there's the issue of CC. Skillshots are balanced around being effects that you can avoid. If you can land one, you'll get a pretty nice reward. Now lets say somebody else lands a stun. This means that your skillshot, a spell balanced around being unreliable, is now totally reliable. It's one thing if there are a couple spells like this in a match, it's another when 7/10 champions in a match have a spell like this. Instead of "Oh I got hooked by Thresh, now I'm going to get flayed into his team and be in a bad position", it's "Oh I got hooked by Thresh, now I get hit by every skillshot nuke on the enemy team and instantly die".