The issue then is Kaguya scrubbed him and left him on the verge of death with near depleted chakra reserves. So clearly they had a battle in which he was far inferior to her. The issue is moreso that prime Ishiki got scrubbed by a far weaker Kaguya to the one that fought Naruto and Sasuke. Then a far inferior Ishiki in a far inferior vessel somehow takes down the two. Truth be told, she was introduced because there was no way Naruro and Sasuke were beating Madara. The writing style is just abysmal, the threat remained secret for so long (1000+ years), and decided to surface today. His deteriorating vessel took 1000+ years to deteroriate, and remained intact (not ageing or decaying). He couldn't find a vessel in 1000 years+ I guess he didn't know Indra and Asura were popping out perfect vessels for 1000 years. This is just the tip of the iceberg with all the problems that arise, because of the abysmal writing.
Then you have what you mentioned about Naruro getting fodderised by Kara members.
You're vastly misinformed.
First of all, Ishiki was defeated off-guard. I'm not sure why people like ignoring this.
Secondly, that very scene Ishiki was shown dismembered, we actually saw Kaguya with the Rinne-Sharingan prior, which means she ate a chakra-fruit. The Rinne-Sharingan only appeared in her case after she ate the Earth's chakra fruit.
Jigen (Ishiki vessel) absorbed the Juubi chakra just before he fought Naruto and Sasuke, so he wasn't far inferior. The fact he beat them silly, implies he wasn't even inferior in the first place. I hate trying to point out people's motive, but it's clear your problem with the Jigen isn't based on objectivity. I don't even need to prove this. You've mostly avoided critical points stated in the manga to make your argument seem more reasonable.
Additionally, the recent chapter showed that Ishiki still has more abilities.
He has a dimension where he stockpiles what he shrink; a dimension where time is still.
This ability means, he could have dimension dump Kaguya there, if they had actually fought in a drawn out battle, and Ishiki would have won.
You should really wait till we know Ishiki full power before assuming Kaguya is stronger than him, and also; try to be at least objective. I suspect you don't even like the sequel, because your favorite characters from Naruto were depicted badly.