You can boost four individual areas of your Thor.
First is his general Strength, which makes him faster and stronger each time you raise a level.
Armor is second and these are new suits of armor that you can don once they're unlocked, either by collecting enough stars in the game or, if the option's available, buying right out.
As for Skills they are used to teach Thor new moves on the battlefield, including a collective hammer spin that can hit multiple enemies at once.
Finally the Weapons section, best mainly around hammers. Of course they get a bit bigger in size than the basic Mjolnir model Thor starts with, and even come empowered with flame, electricity and more over time. Shop around and see which ones work right for you.
As for your allies, you'll basically increase their general Speed and Strength stats, which will serve you better in the long run during later levels of the game.