The ship we've followed throughout most of Star Trek is the USS Enterprise that maintains the registry number NCC-1701 with a suffix change indicating linage.
Does anyone have a really good explanation why other federation ships that have known long lineages don't follow this registry format?
Because it's a Starfleet tradition to do that for Federation starships named Enterprise
. It may have originally started with NCC-1701-A being done to honor NCC-1701, but with subsequent vessels it's more of just an Enterprise
thing in general and a time-honored practice unique to Starfleet, IMO.