I think blizzard is allowed to have at least one hero without fatal flaws without it being called a mary sue.

Anyway, thrall does have his flaws. While being measured in judgment is usually a good thing, a lot of things happened right under his nose, even in orgrimmar, that he wasn't aware of. Things that happened in Undercity while he was in command can also be laid at his feet.

I remember reading somewhere that the man who leads you out of the desert isn't always the best person to lead in building a city, or a nation. I think that may have been what happened with Thrall. His combination of military training, shamanistic skills, spiritualism, and overall intelligence allowed him to free his people, lead them to a new land with a new life, and then to take up the fight against the burning legion. After that, he sets about building orgrimmar. While I'm sure we loved the old org, it's pretty interesting how the new orgrimmar is laid out. Especially with the Warchief's building right smack in the middle of everything.

It can be seen in retrospect how Thrall may have not done quite the job someone else could have; then again, there was no one else (as Anne noted).

Finally, his name is Thrall. His daddy may have wanted to name him Go'el, but he didn't.