Question: Are you switching all the base lists or just some of them? Because, if you are switching them all, why not just play an Armsmaster?
Also, it will take more than just moving some base lists around to make the Magent a more "martial" character. They will need better/lower combat skills costs and maybe change up the professional modifiers a bit, which can only be done at the sacrifice of other skill costs and modifiers.
But, ultimately, rule zero does apply: Do what you want with your game, and above all, have fun. (Or in the immortal words of Abraham Lincoln in Bill & Ted's Excellent Adventure, "Party-on, dudes!")