Every miniatures painter knows that there are a number of games that use miniatures that are already painted. Everything from Heroclix to AT-43 has gone in this direction.
Now, AT-43 and Confrontation minis were designed by Rackham, who have strongly advertised that their minis are 100% repaintable. But it is interesting to look at how much other pre-painted miniatures benefit from some love and care.
I have done a number of repaints from several different sources- including Monsterpocalypse and the now completely altered D&D miniatures line.
There are a few things that you will need to do differently as you approach a prepainted miniature.
First of all, the paint that is already on the miniature is pretty much impossible to remove as far as I can tell (if anyone has succeeded in getting paint off of a wizards of the coast mini, let me know).
Usually that means that the details aren't going to be as deep and defined as minis you're used to painting. That makes the most difference on the faces. It is best to approach a pre-paint's face already knowing where all the details are. Paint the eyes as if they were freehand, and add in the highlights to the places you know the highlights need to go (the cheeks, forehead, nose and area below the nose- etc.). The sculpts just aren't detailed enough to guide you through the painting.
The second problem you'll run up against is that most of the sculpts are a little less detailed than the pewter sculpts that you're used to painting. Don't let any of that stop you. There're a lot of great things you can do with pre-painted miniatures. But you have to be a little creative, and be willing to do some free-hand where the details ought to be.
For example, the simplicity of the sculpt usually means that there are broad areas that are ripe to add in some effects. Lighting effects, freehand, blood weathering and starscapes are all fair game.
Here is an example: