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Well, as for City of Lost Children and Delicatessen, I have to disagree and say that I find every single frame of both films a work of art onto itself, worthy of putting in a museum, but everyone has a right to their own opinion.
As for choices and dependencies...
Yes, the easiest way out for the brothers is to say that we (humans) give the machines purpose. However, this is both dishonest and an escape route. The fact is that according to their own myth, the machines were perfectly content as a society onto themselves. They are not like dogs, who seem happiest when there is a human master to please. They are a living species (again, I'm just telling you what the brothers said here, I'm not inventing or interpreting) who want nothing to do with human imperfections and use the humans the way that we, initially, used them.... without compassion, without interest and without any desire to become "involved".
If you think about it, it makes no sense whatsoever for them to turn around now and say that if humans were to not exist, the machines would find themselves purposeless, because the reverse analogy would be to say that if the matrix ceased to exist the inhabitants of Zion would find themselves purposeless. On the contrary, the Zionites would like nothing more than to not have to worry about machine invasion and long for the day when they can return safely to the surface of the earth to rebuild human civilization.
Which brings us to "the choice." The architect doesn't have to offer Neo a choice. He can (if he wants to) simply explain to Neo that humanity serves one purpose and one purpose alone... to power the machines civilization. In the same way that we would not negotiate with or give choices to a malfunctioning nuclear reactor or hydroelectric dam (we would tear them down and replace them), the architect can explain to Neo that the prophecy was put in place to misguide the anomaly and bring it, again and again, to this place where it can be deleted, and the people of Zion wiped out. Period.
The explanation (as I interpret it) for why Neo is being given a choice is that the whole program for the matrix is based on allowing the inhabitants to make choices and for some reason the architect is extending this courtesy to Neo, even though Neo is not a pod dweller anymore and his individual existence is, far from being critical, rather, a nuisance and a hindrance to the machine's survival.
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