Well I just thought of something.
I have a feeling that the alliance is running out of chakra, because ever since they gained the Kyubbi cloak, they started using chakra taxing jutsus out of their league. Now that the cloak is disappearing, they basically overused their own chakra reserves along with the cloak. Also now that the cloak is disappearing, these cloak beholders are feeling their chakra pulled out of their body, hence they feel like they are out of chakra even though they may still have some left. An analogy of this scenario is when a person takes a stimulant drug to stimulate themselves but when the drug is used up, they feel depressed. As for the Gokage, they were never at full chakra to begin with so they used up what little they recovered after coming back from the Madara fight.
This just sums up my thoughts as to why everyone seems to have low chakra.