I still have hope that Episode 3 is coming, but doesn't look like it will be coming too soon:
From Mojo's trip to Telltale HQ:
I then asked Emily about Bone, and she said that no, it wasn’t getting made at the moment, but everyone at Telltale would really love to do it. “We were talking about that at lunch, actually. We wish we were working on Bone.” She looked really glum as she said this, so I said: “oh, never mind, it’s best not to spread yourself too thin anyway.” I think that there are actually darker reasons for Bone Episode Three not being made, something about licensing, but I couldn’t find anything else about that, as it’s one of those touchy legal subjects. Speaking of which, I made an ill-calculated joke about “market place realities” that got an awkward silence. Whoops!
My suspicion is that they're working on something else (The CSI and S&M teams are just about wrapping up major production right? So something else must be in the works for them to be too busy for Bone?) and they don't want to restart the Bone franchise until they can do it "right," with a properly sequenced episodic schedule.