Welcome, fellow newbie.
I have some advice for you. Don't just jump to a full game project. Do at least one character and one stage to get a feel for how coding for Mugen is like. Once you know the limits of the engine and have some experience, then you will be able to design a set of characters with the same base mechanics.
Once you get to work on the full game, the first thing to do is a design document. Have all your ideas laid out on paper in advance and take the time to plan everything in detail. It'll help you a lot.
Finally, don't make your game just a (insert name of game here) clone. In order to create interest, your game needs to bring something new to the table.
Best of luck to you.
Well, I did manage to create a stage of my own just yesterday, and it's actually pretty good for a first effort.
As for the clone issue, would a House of the Dead-themed Mugen game(which is what I'm ultimately trying to do) be considered a clone game? Even though no one's ever done it before?