Go for the most active one
There isn't one "most active one" because federation isn't perfect and every instance sees a different number of users/posts.
The people on the other, smaller, communities will find out about the main hub and subscribe to it as well.
You can't guarantee that. If they are on a smaller instance, their instance may not be aware of the larger community/instance.
I think decentralized systems are much better than centralized systems, but they're inherently more difficult. Also, your solution (everyone eventually just uses the same community) isn't decentralized. My proposal, which the third solution in the article is based on, enhances decentralization by allowing duplicate communities to exist but consolidate the userbase and discussion.