Losing Spike TV and not being able to convince people it's different now are their biggest challenges. Seems like whenever they've had a great on-screen product since then, people would still just ignore it
We also can't discount the emergence of NXT as a "third brand" and the WWE Network. Before the Network, indy guys would have to decide between a developmental contract and getting no exposure vs going on TNA and getting seen by millions while also getting paid somewhat. Now people are just signing with WWE with no choice.
Losing NJPW as an affiliate to ROH was also a big deal in terms of perception. They actually have better TV deals globally but domestically no one will argue if you say ROH is #2 at the moment.