I love "natural" scenes in quilty projects, and I think your whale shark is gorgeous!
If you decide you don't want a puffy fish (though I think it would be great left puffy, or made even puffier) you can hand or machine sew inside the fish's outline, easing in the extra fabric. You can do this pre-quilting if it is a small area that you would not need to quilt otherwise, or you can do it while you are quilting (I find that trickier, personally).
And I agree that your whale shark fabric is perfect!
Alison