Reddit isn't totally free of this problem (feature) either--You can have multiple subreddits dedicated to the same topic.
IMO while the federated communities might feel fragmented if you are used to reddit, it's the main benefit of using Lemmy and something that should be embraced. Concentrating content into only a few instances defeats the point of federation.
Take the current issue as an example: A gigantic community defederated from another gigantic community leading to a comparatively large wall between the content of those communities. Had they been smaller, the impact of this issue would therefore also be smaller. This affects other communities which get content from beehaw as well, since there's now less interaction between a large portion of the fediverse user base.
It's only natural that large communities will bubble to the top however, and there probably isn't a good answer to how to 'balance out' those communities, or if that's even beneficial at all.
The bottom of that Wikipedia page has a reference to something else that sounded interesting called “/dev/mordor” in some Plan 9 OS fork called 9front. Sent me down a really interesting rabbit hole http://9front.org/