Do you mean that the pattern calls for 16 FQ but you don't have 16 different appropriate fabrics? It's really going to depend on the pattern if that's important or not. If it's going for a scrappy sort of look, you can probably have fewer different types of fabric and still have it look fine; maybe use 8 half-yards instead.
I almost never buy fat quarters, they're just too dinky for my taste. I prefer half-yard cuts at minimum (1 -3 yards is better) and just cut things down from there.