I'm confused by your confusion. :)
> If you don't even aim at having your democratic institutions cooperate, then what are they for exactly.
I think they can cooperate, but I don't see why that means everything needs to be pushed to the federal level? It seems pretty reasonable that local infrastructure should be managed by local governments, state infrastructure by state governments, and federal infrastructure by federal governments.
That said, I'm particularly confused by why you think that the purpose of democratic institutions is "cooperation" rather than something like "maintaining the rights and upholding interests of the public". Cooperation is just a means to that end.