You've stumbled upon the thing that drives me nuts about AGAL/Stage3D. Limitations in the API prevent you from using shared vertices in many circumstances. Wireframe rendering is one example where things break down...but simple flat shading is another example as well.
What you need to do is create three unique vertices for each triangle in your mesh. For each vertex, add an extra param (or design your engine to accept vertex normals and reuse those, since you wont likely be shading your wireframe).
Assign each triangle a unit vector A[1,0,0], B[0,1,0], or C[0,0,1] respectively. This will get you started. Note, the obvious solution (thresholding in the fragment shader and conditionally drawing pixels) produces pretty ugly aliased results. Check out this page for some insight in techniques to anti-alias your fragment program rendered wireframes:
http://cgg-journal.com/2008-2/06/index.html
As I mentioned, you need to employ a similar technique (unique vertices for each triangle) if you wish to implement flat shading. Since there is no equivalent to GL_FLAT and no way to make the varying registers return an average, the only way to implement flat shading is for each vertex pass for a given triangle to calculate the same lighting...which implies that each vertex needs the same vertex normal.