I decided to modify Hairygael's original thumb base.

I used SketchUp and imported the original STL (leftthumb5.stl).
I then only kept the base part and the part that glues on it and after some editing I came up with this :

New thumb

Then I printed it using the UP! :

New thumbNew thumb

Now the thumb's angle can be adjusted and even animated using the same wiring technique that is used for bending the fingers.

You can download this thing here.