Thor: Has a cape, can travel through time, can hear people talking from the other side of the planet, has sick stamina, he can summon storms and thunder and what not, and he has that big.
Captain America: He has super endurance( so he can hit the gym for hours at end and not get tired), he can't drink alcohol at all( lame!), has a vast military knowledge, and he has a really nice shield.
Looking at the comparison above you really have to consider what is most important to you in a super hero. For me the most important thing is the story. Some people compare their super heros on super powers alone, but if you ask me you have to look at the story. If the story sucks then who cares what his super powers are. Anybody can make up a super hero with awesome powers, that doesn't mean you will like him. For those reasons and after careful review I went with Captain America. Now Captain America's powers are really lame and he can't drink booze but his story is interesting. The story of Thor is weird and confusing.
So who do you guys think is better?