I think they need to step up the powers ala what they did with Cap in TWS. I do not want to see Thor look like Superman in MoS, which I thought the effects looked silly and video game like.
Showing Thor's flying ability tied to swinging Mjolnir is great, and an homage to how Lee/Kirby wrote the character. He should not fly like he does as Ultimate Thor.
Don't make Thor strong by making Ultron Weak. In Avengers EMH, Ultron was about to kill Thor, but Enchantress transported him before he was killed.
Ultron can absolutely destroy Thor, as he can any of the Avengers, because he can think faster and knows all of their vulnerabilities.