After much talking over at TAU, Treeform, I have secured consent to try your tool out on one of the best collections of models, and see what results can be had from taking the resulting uvmaps and reworking them.
Here are all of the 3DOs which are Original Works within the project called Talon. The Registered One, one of the many experienced modelers who has built content for the 3DO format, has agreed to let you process these files with your tool, with the understanding that you will provide them to us in a format we can use- i.e., .S3O, or failing that, .3DS or .OBJ, with normals preserved.
If you can get that to work, I will show you guys what can be done, very quickly, if I have a model that's pretty much ready to use, minus minor alterations to the uvmap. Again, there's a reason why I'm excited about this topic.
Before the other creative artists at TAU are likely to release any other work for you to play with, though, they would like to see some proof that this isn't a waste of time, and they also want to see your tools- what you've shown us thus far looks like a very powerful tool, but people aren't going to trust a stranger with their content, using tools they've never seen before. If you're reluctant to share the software, I may not be able to secure anything from the other copyright holders.
@zwzsg: you could make a very large DDS file, by simply combining every 3DO in a given collection together in one S3O, so that every texture you use will become part of the final picture. Nobody's tried that yet, but in theory, it should work.
However, what you're forgetting, I suspect because you don't have much experience in uvmapping, is that what's wrong with 3DOs is that the textures are being distorted across the quads. What Treeform has built is a method whereby the resulting surface normals aren't being distorted, which means that, if I want to perform mirroring or stitching operations on the uvmaps, it's really easy, since I can identify the quads by shape if nothing else. What UpSpring does is to force all quads to become squares, projected through a small square of texture. This saves texture space, but doesn't provide a very accurate set of projections, and is completely useless to reskin with- it'd be easier, frankly, to just take it all into Wings and build a whole new set of projections from scratch, frankly. Which is exactly what I'm trying to avoid here, because that's where the time-cost is the worst...