Asked if The Binding of Isaac: Rebirth would have a publicly available level editor, designer Edmund McMillen responded, yeah, that might eventually happen.
"The editor won't be in a state to go public so we won't be releasing it," he wrote on Tumblr. However: "If we do DLC and people want it though I'm sure it will be updated, tuned, and added in as part of whatever DLC we do."
Presumably, such an editor would allow us to build a pool of custom room layouts that the game could draw from for each procedurally-generated run. And that would be a marvelous addition, if you ask me. That and mod support. Mmm, Rebirth is going to be a treat.
If you haven't been keeping up with the game's blog, you're missing out.