Two words: Telegraphed Skillshots
Everything Pyke does gives you a warning before he does it. His skillshots are thin and give you more than enough time to dodge them. If he lands his abilities after telling you he's going to throw them out, he outplayed you, plain and simple.
You shouldn't be trying to kill Pyke in the laning phase. Go after his carry. Until he gets items and levels on you, Pyke has hella-long cooldowns and doesn't have the damage to get kills on his own. He can set up the kill and finish it, but he has a lot of trouble with the bit in the middle. He depends on his carry to do that. He has no heals, shields, or utility for his carry, so you have an easy time poking them out and making it unsafe for them to take trades. If you force their carry to be on the back foot, Pyke gets no value because there's no one there to follow up on his CC.
Pyke also has terrible waveclear, and his hook is blocked by minions. Push the wave into the tower, and you get a wall of minions to protect you from Pyke, and he can't help the carry shove the wave back out or keep it from crashing.
Through the mid and late game, Pyke quickly becomes one of the squishiest things on the planet. He can't build health, his armor/MR scaling is pretty crappy, and he needs to build Lethality items to scale. Once you start teamfighting, NOW it's time to start focusing down Pyke. If you can CC him, he's dead in the water. He'll need to start saving his E to get OUT of fights, since his W doesn't make him totally invisible until he gets far enough away. Focus on killing Pyke first in teamfights so he can't clean up the fight with his ult. Past the laning phase, Pyke is made of paper. He can regen if you let him get away, but if you catch him out, he evaporates.
If you're going against Pyke, consider buying Boots of Swiftness to make his hook less punishing. He's going to buy a ton of lethality in 90% of games, so buy health items instead. His execute is a flat value, so the more health you buy, the harder it is for him to kill you. Taking Heal is a great way to counter his ult, since the burst of healing can take you above the threshold, forcing him to commit his own summoner or another cooldown to continue chasing. An enchanter that does a lot of healing or a tank that does a lot of CC will be Pyke's worst nightmare.