The biggest problem you will have is the cliche problem. Far too many people will use it as an excuse to hate yoiur comic, and so this needs to be discussed.
A cliche is anything that has been over-used. You know: magical girls, card games with living monsters, giant ships with bigger guns. Something that you see way too often.
Cliches tend to be used either by beginners or commitees. For beginners, cliches allow them to stay in a safe area, roughly akin to bunny trails and shallow areas. There's very little danger, and they know the curves. For comittees, it means a guaranteed success; after all, the idea has proven itself over and over and over, and works as new viewers who haven't seen it but saw the old generation like it. Yes; an entire generation that hasn't seen Card Captor Sakura, and to whom the magical girl show is actually new! Weird, but true. And it's that new audience that allows cliches to be perpetuated.
So...how do you avoid cliches? Think it through and plan. If the idea is that you will fall back on cliches when you need something safe, don't put yourself in a position where you need that fallback. By planning ahead, and taking an honest look at your script, you can avoid the vast majority of cliches.
Also, know the industry. Before you get really interested in your idea, take out a piece a paper and list every comic you can think of that even looks like your idea. if there are more than a handful, then odds are you're dealing with a cliche. Another way is to go to your favorite comics spot (like Buzz Comix or Comic Genesis), and use keywords that would apply to your comic and see how many comics pop up.
I point this out because far too many beginners replicate almost word-for-word ideas that are just a few years old, and then get quickly frustrated when a number of people point out that their great original idea is already cliche. The best way to avoid this, obviously, is to know what has gone before you.
Hmm...Guess some examples would help....