"No glaring weakness for him to take advantage of"
First off, it doesn't have to be an explicit weakness, Luffy's pain tolerance, elements of surprise via unpredictable fighting style, homing attacks, and future sight will allow him to see which techniques counters Nagato the most, either it's long range, close or mid, then adjusts his strategies accordingly to take advantage of what he learned and that in a split second to, furthermore the longer the fight the faster gets snakeman though speed is equalized, but he will just find out more ways to hit Nagato, but when it comes to stamina, Luffy is superior.
Chibaku Tensei's weakness has been revealed by Itachi himself that long range attacks aimed at the epicenter of Chibaku Tensei is it's weakness, so don't get me started with Luffy's superior lifting strength. Also, before anyone says it required all three to destroy the Epicenter of Chibaku Tensei. When Itachi wasn't sure himself if one powerful long range attack is suffice, considering he doesn't like taking risks it makes sense for him to ask Bee and Naruto to throw their range attacks as well, unless you wanna argue the epicenter of Chibaku Tensei is Island lvl, instead of the completed version.