The Metadata system in spigot is a very powerful way of keeping information. It's nice, it's clean, and it does what it should.
Unfortunately, it resets on reloads / restarts! If it weren't for that all developers were using the Metadata system. That's it's only flaw.
With players, there's already a player.dat file - why not save it there?
As for blocks, spigot could create a new blocks.dat file to save metadata and reload it on restarts/reloads.
This would be a major addon to spigot that would help everyone!