You can lessen the need to wait for the battery recharge by activating your Zonai power cells you will see more battery symbols appear on screen indicating the extra batteries life,they will considerably lengthen the time depending on how many of your Zonai power cells you activate and like the extra stamina it stays with you till its been used up.
I'm still on Sky Island, I didn't understand half of what you wrote up there ;) I have one battery and a couple Zonai things left over (traded most in for fans and wings), no idea how to use them. I guess you mean the things the guardians drop? Which I have been dropping into the dispensers.
Anyway I made a soft landing (pushing those platforms down takes a lot longer than up) and left Link at the entrance of the shrine. I guess my 'air ship' will be gone when I get back out (bloody thieves everywhere!) but there's a take off ramp to fly back I assume.