Really, my own preferance, and the one I think will get you a better story, would be to NOT have a system.
I feel like a system take away from the story. Systems fics can be fun, but they actually stop you from exploring your character's powers or finding interesting and gratifying ways of solving issues. You are either capable of creating a skill for any situation, or your character is locked into a class and, the vast majority of the times, the skills are set.
The worst is in the end game of your story, where your character tend to either get ridiculously powerful and versatile, or it feels like he hits the "Level/Stats cap" and it makes your readers, who are used to the growth, feel like there's no progress.
Another point is, do you want to give your character a specific power? Because it would be much better to give him That power, and then have him deal with situations with that power, instead of giving him a class and making it a skill, it gives you more freedom to explore, and more freedom to play with limits or things that empower it, to be more creative in the power use.
Again, there are good system stories, and a system can be an easy way of showing progress in a story, especially when you don't actually have an entire story arc in mind, but it can feel like a crutch.
So, unless you especifically WANT to write a system fic, (and you don't seem to have that as a goal), I REALLY suggest not using a system.
... On the other hand, I have to warn you, it really seems like it's easier to get readers with a system story.
I mean, there's a lot of people who won't read system stories, but even people who don't particularly like it tend to at least give a story a try, and there seem to be a lot more people who actually look for it.