I would rather like to see them continue operating like "be different, but together" so as to give a choice to users to either use the most cutting edge APIs or more stabler versions. Node.js could be like RHEL/Ubuntu LTS, where as IO.js could be like Fedora/Ubuntu Latest.
Exactly, I recently heard the nodeup podcast where it was said that io.js is beta and don't expect rc-1 or beta tag, just plain semver, but said that eventually both forks should unite again. That plus update-on-release V8s are incompatible with Joyent's "enterprise grade tested" releases.
The only way that this will realistically work is if it falls under a single project. But hopefully the formation of this foundation will lead to a cohesive platform. Its fine if a small team or single developer runs a canary setup; at larger scale development it becomes very difficult to coordinate when its right to run LTS versus not. You'll always default to running what's on production.
That's what's happened with Scala. Official Typesafe Scala is for enterprises and the fork by Typelevel is for faster development and experimentation, with a goal of contributing the things that work out back to main Scala (if Typesafe accepts the pull request).
The Scala landscape is pretty far off from the node/io fork, I think. First of all, we are keen to keep Typelevel Scala and the official Scala distribution in synch. We're also seeing a healthy acceleration in contributions (proposed & merged) over at https://github.com/scala/scala#welcome -- all contributions welcome!
In any case, we're happy to see experimentation over at Typelevel. If you're interested in this kind of stuff, I'd recommend also taking a look at https://github.com/non/cats.
I think most people are using the main Typesafe Scala, but people who really want to probe the depths of what Scala can do are using Typelevel's fork. As far as startups they are probably using regular Scala unless they've found something in Typelevel's fork that they need.
Unlike the Node / IO situation Scala has always been run by a foundation and continues to have key players on both the main branch and fork.