Just spitballing an idea I haven’t fully thought out: One interesting way to avoid excessive centralization may be to display a “Join lemmy” button to logged-out users, more prominent than the “Register” button, which redirects to join-lemmy.org/instances instead of the instance registration page. Though I agree with your point about join-lemmy in its current form being somewhat underwhelming as an onboarder. In addition to what you mentioned it could do with some filters (For language, at a minimum) and sorting (For instance age, size). Even adding a button that basically says “I understand the instance I pick isn’t that important, just send me to a random reliable one please” would help a lot.
In the long term I also hope Lemmy evolves to actually make the instance you’re on matter less - for example, by changing defaults on the homepage and search page to “All” instead of “Local”, showing global subscriber count instead of instance subscriber count when searching communities, adding ways to migrate accounts and communities between instances, and perhaps even adding a way to merge one instance into another if one admin no longer wants to maintain their instance, and another admin is willing to absorb them.