Decentralization is tricky. Bluesky chose a central firehose for this very reason - and thus setting up a second Bluesky node is incredibly expensive. Mastodon tries to do "as good as it gets" without the expensive part.
I think the development currently being planned by the Mastodon devs to fetch all known replies at the origin server when we click a post is a great step forward, but it won't help with discoverability and search.