I think you've correctly identified a problem, but misidentified the solution.

It's true that there are many redundant communities of which everyone would be better served if there were an easy way to group them together. The solution, however, is not to reduce the number of instances, but rather to provide more tools for instances to group communities together. You want communities to be spread across many instances because this maximizes user control - it's kind of the entire point? But of course, the lack of grouping makes it very difficult to try to centralize discussion, which is important for the community to grow. This service is still a work in progress, so these kinds of things - I hope - will come in time, as both the technology and culture develops.

tl;dr: centralized control bad, centralized discussion good, the current system does a bad job of reconciling these two positions