So, I admit that I'm late on this, and sorry, but I'm going to be late on the next one too. It takes a while to go through this....
I'll come out and say this outright. I loved Thrall during Warcraft III. He was actually the reason why, when I looked at Vanilla through half of wrath, I was actually fairly sympathetic to the Horde. I played a different character with neutral events and a neutral personality. I defended the strengths of the Horde and ignored its failures. I didn't like Varian at first. My current position really came into focus when I ran into a Horde RP-PVPer on another forum that I used to frequent who shifted the blame for rather jerkish behavior to supposed atrocities that the Alliance was responsible for in his mind. One thing led to another and I started to realize that Thrall is actually sort of a jerk himself for letting his people really just get away with murder.
The problem is, I don't think it was intentional.
In Warcraft III, Thrall was the peacechief, but he also knew that he needed to keep his people in line. I loved his relationship with Grom, for example. Sure, he was peaceful, but he was willing to work hard for that peace, whether it was against admirals who couldn't see past the second war, or glory-hound Orcs within the Horde. So what went wrong?
I was a teenage plot device
So, in Warcraft III, the Night Elves are in the Alliance apparently only for the point of conflict. Why does Thrall ignore this? Because he has to in order to make the plot to work.
We get Garrosh and he's acting up. Why doesn't Thrall reign him in like he did with Grom? Because he has to ignore it in order to make the plot work.
Sylvannas is very clearly doing bad things for a while. Why does Thrall ignore it for so long? Because he has to in order for the plot to continue.
Seeing a pattern?
The character sort of just up and died from the word go. He's not really the strong guy who knows that peace is what's best for his people and strives to make it happen, and even though at the time he was still so loved, he was kind of just there... or not there when the plot needed him to.. not be there.
Then Cataclysm happened. I don't really think that this deserves its own bullet because it's been done to death. It's the problem of a Blizzard protagonist also being either A. Metzen's self-insert or B. Blizzard's bully pulpit, or C. Both. We've seen far too many superman like characters who hog the spotlight who can do know wrong, despite being almost universally hated by the end. I don't want to dwell on that though. This is about how to fix him.
Peace... not at all costs.
The siege of Orgrimmar leaves us with a problem, a big problem. The Alliance should not theoretically be able to stomach the idea of leaving the Horde attack after everything that's been done. Really, I think that this is where Thrall can shock and amaze us, by turning the rebellion on the Alliance, alongside with the Kor'kron, who side with him and kill hundreds of Alliance soldiers. The leaders of the Alliance see this as an outrage, but Thrall sees it as necessary to preserve the Horde. We don't see talks at this point, and we don't see an end to the war. It simmers with both sides having justifiable reasons for their war, and some escalations that are a little harder to justify.
Perhaps this is more of a fix to the world, but I think that this would be a good fix for Thrall as well. It gives him controversy and possibly some doubt over what he's done, but the bigger point (so long as the Earthen Ring doesn't get dragged in - please avoid that) is that Thrall becomes a Horde character again. The reasonable Horde warchief who wants to see things improve, but isn't afraid either to defend his people.