All creators can testify to the satisfaction of making a character for their comic story. And for the most part this is fun and always interesting. Most indie characters end up on a self published comic of some sort and usually make their debut in a local comic convention or two. These characters face many perils in their story but none as devastating as success. You see once your character becomes popular you begin to gain many secret enemies. And their weapon is intellectual copy right infringement!
First thing you need to know if you plan to make a professional character for a commercialized story, comic that you plan to sell, is that there is nothing new under the sun. What I mean is that there are many variations of existing ideas. what's very important to know is that you try to take very obvious elements from other characters...satire being the loop hole in all of this.
One of the fist dangers is comes from the origin story. Have you noticed that there aren't many "Super" anything outside of DC or that the term "Mutant" tends to stay within Marvel as "Metahumans/sapiens" deals with super heroes in DC. These coined terms are some of the few ways large publishers can trip you up when you begin to head towards a recognizable amount of success. Magic and religion seem still pretty open as most big publishers barrow from Greek mythology and various religions...especially in today's hot topic arena. Topcows uses technology to explain their characters super powers and a touch of religion and magic as well.
When you start talking about where you characters get their powers, remember where the land mines are and choose a unique way to explain the source of their abilities or keep it a mystery.