Some instances are running on better servers than others, have staff that fix issues quicker and attend to updates sooner.
For example, .world is still on v18 while the rest of the threadiverse has mostly moved on to v19.
Some instances defederate certain other instances, so in some cases you might end up finding that a community you subbed to gets disappeared by the admins of your instance (lemmy.ml did this to ani.social a while back). Whether there are valid reasons goes case by case, sopuli.xyz for example blocks instances that are for porn, and I like it that way.
Though outward federation is a bit borked on there atm, so I’m using my alts…
But really, it doesn’t matter that much. If the grass looks greener, you can hop over the fence and see for yourself, and then hop right back if it turns out it wasn’t.