There have been public complaints from Blizzard employees about Battle.net. Community managers and developers both have stated that improvements to Battle.net are far harder to push through than changes to the games proper. Why exactly this is, I'm not sure. My guess would be that it's either seriously understaffed or drowning in bureaucracy.
I can see it being more difficult to modify, since it powers all Blizzard games. That also raises another option - it's a technical mess that no one wants to touch...
I'd bet it's drowning in bureaucracy for a reason — Battle.net is a common component in virtually everything the company creates, so any change to it will impact a lot of people's work in unforeseen ways.
Well, still (or perhaps even more so) - if they considered something like chat rooms to be as essential as many users feel, it would have been easier to implement earlier rather than later, when there are more products to support.
Then again, something like chat rooms could be implemented per game, minimizing impact on the entire battle.net system.
It just wasn't seen as a priority, or there wasn't the political will to push it through, or there's something else we don't know.
