Farm system rankings are still coming in, as Baseball Prospectus has published theirs. It’s a subscription site, so I shouldn’t go into it much; the writeups are pretty brief anyway.
The punch line is, BP has the Pirates at the top. They have some reservations about the pitching being risky, which of course it always is. But they see the system as the deepest in baseball, with four top-50 bats and lots of guys who could be good regulars.
These rankings can have some interesting quirks. If you remember, Keith Law had the Dodgers first and Jays fifth.