Thrawn is better than the Sith for the following reasons:
1) His cause is just, in his own eyes. His goal is to bring stability to the galaxy, not to conquer or oppress. He believes a strong imperial government is the only thing that will save the galaxy from further civil war and chaos (what followed the death of the Emperor). This is why you can empathize with him, even if you disagree.
2) He is an alien stuck in a xenophobic Empire. In case anyone didn't notice, the Empire was entirely human. He rose to power in the navy based on his brilliance, even against massive resistance. It's like if Hitler died and then a Jew become the new Fuhrer. You know he means business.
3) He is a genius. He is able to predict the actions of others based on their racial and cultural identity and backgrounds, and on top of that is a brilliant tactician.
4) He has creatures which can nullify the force in short range, making the Jedi useless.
However, here are the weaknesses of using him in Star Wars movies, where you need to dumb things down:
1) He is too grey morally. He needs to be evil to be the bad guy, which is why I expect the cheap cop-out of having the Emperor's force ghost appear as the villain. The Star Wars movies don't tolerate moral relativism, they require good vs evil.
2) He doesn't use the force, in fact he uses tools to suppress it. This means no lightsaber fights. Marketing requirements demand lightsaber duels.
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I fully expect the sequel trilogy to be much better than the prequels, and there's a chance they could be as good as the originals (taking nostalgia out of the equation). However, they will never be as good as they could be purely because there is now a Star Wars tradition and people will be too afraid to break it. That is why I expect the Emperor to be back, the Sith to be back (a battle in the nether world perhaps, the dead Sith vs dead Jedi?), and I wouldn't put it past them to have a death star...or maybe ghost death star.
