The problem was that Node was based on a way older version of V8 with little sign of being ready to move on in the near future, and io.js users had access to all sorts of new features, so it was not a good thing for library authors - either you use the new features, and nobody using Node can use your library anymore, or you keep compatibility and have no advantage over just having Node.

They weren't really different implementations anywa - io.js was based on Node and most of the work they had done (as far as I know) was the move to the newer V8 engine version. So they were the same thing, just partially incompatible!

So it's really a great thing that they're merging, because it means that many more people can start actually using the new stuff!