What I'd like to say to you is not to worry about whats cliche and what isnt.
If theres one thing I've learned through writing fics, its to write what ever you want to write, and dont write around popularity. If your writing style is good and original, there is no reason for people to dislike your story, even if it does include cliche aspects, becasue no story can be identical to another unless, of course, its intentional.
If you want to write the story with Team Magma, then go ahead and write it. What it all ultimately depends on in how you write it, be it through skill, plot, portrayal, whatever.
However, if you are perfectly comfortable with writing about another team, and you'd rather do that then write about Team Magma, then I'd suggest creating your own. Perahaps even make a spin-off from Team Magma.
I'll follow this thread and help you more if need be.