It'd be nice to be able to store data for items etc. and have it be persistent across restarts. Perhaps have a 'plugins' tag either under the 'bukkit' tag or independent of it that is accessible via methods in Bukkit/SpigotAPI. Also have the relevant Minecraft NBT classes exposed for ease of use (they don't change much.) I haven't looked at the NBT code recently but once my CLA request goes through I could look into something like this myself.

That or have something similar to Bukkit metadata but have it be persistent.