A few days ago, Bashiok stated the following:
We actually have moved on from the previously discussed unattuned system. We’ve been trying many different ideas out, but we’re not quite comfortable enough with any of them yet to invite you in and see what you think.
Let me also say that the old system wasn’t broken, per-se, it just had a few issues we thought we could resolve. Runestones are a huge part of Diablo III, and we think it’s worth trying out some alternatives and see if we can’t improve it. But if all of our experiments fail we can easily go back to the original system, and it will still be totally awesome. (Source)
Now, whether that means we may see the rune system in the beta is yet to be determined. This may only mean that we’ll get a preview of whatever rune system they like the most via the community site like we did with so many other systems. Lets collectively hope for more beta content.