Because high skill cap champions have more options so they are easier to play in some scenarios.
Let's use azir as an example. Arguable one of the highest skillcap champions in the game. He can - poke in lane well, all in well, has decent mobility, has engage, has a strong early and lategame, and has long range. If he gets ganked he just dashes out. If he wants to engage he dashes in and ults.
Let's use annie as another example. One of the lower skill ceiling champions in the game. She has burst, and that's about it. It's not even super strong burst unless she's fed either. If she gets ganked she dies if she's not warding properly. If she wants to engage she either has to play around vision or have flash up.
TL;DR
Does this make azir super OP? No. He's hard to play mechanically. You have to understand how to play azir well when you're playing azir, whereas when you're playing annie you have to play the game well.