I can't even begin to defend the movies. At the end of Reloaded I thought the big revelation that Neo had that made him go into a coma after miraculously stopping the squids was that they were inside another matrix in the "real world", and that his coma was him finally getting out into the actual "real world". This would have helped explain the humans as batteries thing. That never happened, and I laughed in disbelief at how horrible the 3rd movie was.
I will say that it seemed to me that going above the clouds knocked out all electrical systems in the hover ship. It seems like a bad place to be if you were a machine, some sort of EMP effect. Also it would be hard to get anything above there without having several lightning strikes too. But, since one of the Wachowski "siblings" was having a sex change crisis during the last 2 movies, that sort of explains things for me, oh well...