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Minecraft Vanilla is normal minecraft like you run on your own computer. Spigot is a modded version of minecraft, with the difference of supporting plugins and having better performance. The default settings of spigot don't do anything except better performance and bug fixing.
If you want plain vanilla, no fancy things like world edit, You should use vanilla. If you want to build your own community server. Your better of with spigot. If you don't need plugins right away, no problem! You can add plugins as you go.