Weapons: Storm has control over the weather and levitation. Thor, being the God of Thunder, has his hammer, Mjolnir, and it’s all he needs. It can create lightening like Storm’s, and hit things really hard. Both can fly, but Thor can fly faster. While Thor can’t create weather like Storm and a hurricane or tornado would probably throw him off, Mjolnir is more powerful.
Defenses/weakness: Storm can create wind and lightening to defend against various attacks, but that can’t stop Mjolnir. Thor has virtually indestructible Asgardian armor and an ultra-dense skeleton, although he probably won’t enjoy being struck by lightening. Nontheless, Thor wins easily due to his immortality.
Skill: Thor knows what he’s doing and is highly skilled with his hammer. Storm as very precise control over her weather manipulation and flight, but her skills are no match for Thor.
Mindset/intentions: Storm works for the X-Men and is doing what she thinks is the best for mutants. Being a warrior rather than a mastermind, Thor tends to focus on the fight at hand rather than the bigger picture. Storm may or may not want Thor alive, depending on what Cyclops told her to do, while Thor just wants to fight it out. Storm wins here.
Use of surroundings: Storm is known to hurl things around with gusts of wind and exploit her surroundings to her advantage. Thor does, too, but less than Storm. The difference is significant enough for Storm get the win–in this category, anyway.
These two aren’t very evenly matched. Thor is immortal (most of the time) and his hammer gives him a lot of power. Storm has the weather at her command, but is vulnerable. She could give Thor a run for his money, but she couldn’t kill him. If all else fails, Thor can tire her out. The fight would be a short one: They would fly around smacking thunderbolts at each other for a while, Storm would probably electrocute Thor, but he would throw his hammer and kill Storm. Thor would be knocked out and injured, but he would walk away victorious.