Well, actually...would your kids like Nemo more than the FL rides? Since they are older, and, one would imagine, easier about waiting in lines, that's something to think about. IMO, at least.
It's prevailing wisdom that you use MM for Fantasyland, but if those rides aren't THAT big a deal to you guys, maybe using it for Nemo would be better for you?
But to answer your question...if you get in line for Nemo after you've already done Fantasyland, the line is going to be longer. Of course it's only going to get longer once the general public gets in. I got in line for Nemo around 5ish last September, and it was about 30, 35 minutes of line (and I find the line to be a fast moving, pleasant, line), totally doable.
Now reading your question again, do you have just one MM day? Or do you have more, either through a ticket from getawaytoday.com, or by staying onsite?