Backfill is one solution. FEP f228 implemented by a bunch of software allows for entire comment trees to be pulled in so you can see the entire conversation. For now Mastodon only implements the serving of the backfill data, doesn't consume it directly.
The other part is discovery, as you mentioned. Using relays and specific tag subscriptions via FediBuzz (@astro@c3d2.social) and tags.pub (@evan@cosocial.ca) get you part-way there.
Putting together a pseudo-centralized "trending content" service is technically sound but at least on the fediverse, socially dangerous. One will get ostracized but some very vocal and very mean individuals.
@albert_inkman@mstdn.party