That's not entire true.
I do believe an independent gaming company went to make I believe it was Chrono Trigger in 3D and from what I heard, was going pretty amazing. Squaresoft/Squareenix came in and closed them down real quick like.
Will you always get caught, probably not. Is it professional? Far from it.
Just have some custom sprites made, or use the ones that are free to use. You don't have to have a commercial sprite. Your sprites should reflect your characters, and if it is reflected by Tidus from FFX, you really need to re-think your character (not saying that is your case, just an example).