You know I have been thinking about this for some time, but I just watched the third instalment of the Trilogy again yesterday and decided it was time to ask the community.
The humans pulled operation DarkStorm to cut the machines off from sunlight, then the machines couldn't relly on the sun for energy anymore and had to find a new way to get electricity and they found something, us. Now, this is where it gets interesting, as we can tell the machines obviously have very advanced hover abilities and construction abilities (look at 01) right? Well when Neo and Trinity are on there way to 01 they quickly fly over the clouds which I think prooves that the cloud covering is reachable.
Now why didn't the machines just build a couple of really tall solar collection panels that reach out over the clouds? Then they wouldn't have to deal with us.
The only problem, I could produce myself, that I had with this theory was that obviously the DarkStorm is electrically charged right? Because it shut down the hovercraft and the other sentinels. But if it has some form of electricity then the Machines shurly could find a way to harness it aswell. Basically I think the hassel to build a simple construction is far more efficient than have to deal with the Matrix and a crap load of rebels, but then we wouldn't have a movie, would we?
Just a thought that has been bugging me for some time. 
Laters



