Kaguya killed him and ate the fruit for herself, right? So why is it that he's still strong enough to stomp on Naruto & Sasuke? How can Isshiki be around Kaguya's level(or higher) despite not eating the fruit? How'd she beat him in this case? He's restricted by his host body too. Are Naruto and Sasuke just that weak or is Isshiki truly powerful?
It's a little bit of both.
years of peace. Isshiki has his own 10tails with him to gain chakra from time to time. Kaguya's splitered 10tails has been absorbed by Momoshiki (so either it is residing with Boruto or just completely gone altogether).
Jigen/Isshiki also have been getting more and more powerful.
My main issue is that why didn't he make a move during the Alliance War or the Momoshiki invasion?
Also we can't really say anything about Kaguya's power level in this iteration.
Kishi's Kaguya, like most females in Naruto, is pretty trash. I'm sure Ikemoto/Kodachi will actually move away from that idea and actually make her somewhat useful