Summon Aery vs Arcane Comet - a detailed comparison
It seems to me that a lot of people think Summon Aery is always better than Arcane Comet no matter which champ or situation you're in. I disagree strongly with this position and I'm presenting an argument that both keystones have their place. I will go over a lot of details to show my reasoning.
Power Curve One of the major differences between these runes is their power curves, that is, their relative power over the course of the game. Aery is better at early levels for reasons I'll go over now. Comet is better (for champs that can use it well) mid and late game.
Summon Aery has pretty weak scaling, but it's pretty strong at level 1. I think it's definitely better for lane harass for the first few levels on basically anyone, but just doesn't scale that well.
Arcane Comet naturally shines in teamfights when used by AoE mages so it becomes more relevant just by its mechanics after the laning phase ends. It also has pretty good scaling.
Stat dependence Another major difference is that while Comet does have good scaling, the base damage isn't great. If you try it on a support and you get standard support items with low AP you'll find it pretty lackluster. Aery is hands down a better choice if you are not going to build much AP or AD.
Reliability Comet has this stigma that people will just dodge it. However, in my experience it averages to 80% accuracy most of the time. There are exceptions, like if you are Comet Ezreal laning vs Janna you will miss most of them. :( So don't do that. Otherwise, if you have a slow and you're against most champs you will see about 80% hit rate. Of course, Aery will have a 100% hit rate so for lane harass over time that's a big advantage. That's another thing that puts Aery ahead for lane harass on most champs.
Teamfights AoE mages can trigger several Comets in one fight due to the cooldown mechanic so this is where the rune really shines. As mentioned, it actually scales well too.
Aery barely does anything in teamfights because it's limited to more or less a fixed cooldown and each activation is low impact. By the time teamfights come, its poor scaling also reduces its teamfight effectiveness.
Champion Compatibility I believe Comet requires a lot of spell hits to take advantage of the cooldown mechanic in order to be strong. So I don't think it's actually optimal on Lux (often cited as a good user) while she does have a root, you just can't take advantage of the cooldown mechanic very well so you won't be shooting enough comets. I think Aery is great on her because it makes her E Harass so much more ... you know... :/ "fun" to play against.
I find Comet works really well if you have a lot of spell hits and some slows or CC. You don't really need a root or stun as badly as you need a lot of spell hits, but I do think completely lacking any slows or CC hinders its effectiveness.
Aery is a lot easier to find good users for. It just does its damage on a relatively fixed cooldown and there isn't a huge amount of gameplay optimization or anything. It's almost never a bad choice. But my point here is that for many champs there are more optimal choices.
Summary Aery: Lane harrass, early game, supports/lane bullies Comet: Teamfights, decent scaling, AoE mages
Edit: I have updated this post by removing the bit about Aery choosing whichever damage type would do the least damage. This property was removed and it now behaves like other adaptive damage sources.