Arcane comet from my experience does a little too much damage early game. This is specifically true in combination with poking type abilities (ashe w, mf e/q, if the q works on comet honestly I'm not entirely sure) and it also works really well with tanks (like malphite, olaf, and I think maokai, there could be a lot more that I missed).
I think press the attack just does too much damage early game currently. I don't know what to say about summon aery since I honestly don't play against it very often at top lane.
There are some other runes in the domination, sorcery, and precision that are contributing to this amount of damage. Coup to grace (which is getting nerfed) gives too much damage while also having a secondary effect after you kill someone. Last stand I think is a little too strong on the dmg part too but i'm not sure yet, I don't think a lot of people are using this rune due to coup to grace so it's hard to really evaluate that rune. This is the same with cut down, but the damage on that row could all get a slight reduction. In the domination row, there is electrocute which needs a nerf I think. Dark harvest I think is kind of weak atm but that might be mainly due to how early games end. Predator I think is still a little too weak and it is gated on cd.
Sudden impact I think is op and it needs a nerf. 10 free lethality and 8 magic pen (I forgot if it was adaptive) is just slightly too much, especially since about 50% (forgot if 40 or 50) is usable in the early game. The takedown passives Imo was a bad idea since it just rewards teams that are ahead while crippling teams that are behind. The middle row is weaker compared to the two and I think it is balanced.
Idk much about how strong the sorcery tree is except for the manaflow band rune. This rune, needs a nerf. I mean, pantheon no longer has any mana issues with this rune if he plays it right and doesn't q minions. The ultimate hat and nullifying orb are probably balanced (idk much about nullifying orb, never really played vs it at top lane).
Probably the 1 thing riot really needs to do to lower damage is to give everyone MR. Seriously though, so many champions that did magic damage who didn't go spell pen are doing too much damage now. Teemo being broken is probably a result of that (he was probably too strong before, and aerial is breaking him a bit, but the no magic resist is escalating this issue). Supports at bot lane who didn't go for the spell pen are now even stronger. If I am correct, most people got to like 8-9 spell pen. So, you actually had a net loss of about 3 magic resist in this case.
TLDR: Arcane comet and press the attack are too strong. Many runes in precision, domination, and sorcery are currently too strong on the damage department.