I'm hearing a lot of Disney blame. While the deal with Disney was definitely the catalyst for these things to happen, I don't think they're the ones to blame. Remember, Kathleen Kennedy is in charge of Lucasfilm now and it's no doubt she's the one behind this shake up. Remember, Disney left Lucasfilm to run pretty much autonomously. She reports on what they're up to but I don't think Disney has an active hand in these decisions.

Earlier an idea struck me. In the last arc to air for season five of the Clone Wars, Coruscant's level 1313 was a pretty dominant setting throughout. When Lucasarts made the announcement for 1313 they also mentioned that the characters in the demo were placeholders. Originally 1313 was supposed to be a tie-in for the live action series that has since been put on hold. I have a strong suspicion they might now be reworking it to feature Ahsoka during the dark times between trilogies.

As for the unaired Clone Wars episodes... I doubt we'll just see them end up as a bonus on the season 5 video release. I think they'll either turn it into a big streaming event on the official site or they'll end up airing on Disney's XD. There's also the slim chance they might cap the series off by editing the remaining episodes into a final feature film to tie up the remaining loose ends. But I wouldn't hold my breath.