I always got mixed results from exporting skin weights. In the end I usually ended up repainting the weights after attempting to save working weights for similar topologies/UVs on canned riggs. The only working examples I can think of where on models that where in the same uvset, combined geometry and the texture size cranked WAY up in the options. Still, my current model is in multiple pieces and has altered UVs because of the manual reduction I did for the LODs.
I'm not sure about cluster weighting because its the same problem as using the Wrap deformer. The skin weights wouldn't be pass threw they would be an internal Maya node that wouldn't export into something a game would use... unless it was ID tech then I could just do it all with blend shapes =P but I wonder if I'm over simplifying the logic and missing out on a process I should look into.
The Vertex color sounds like it could work because it could be scalable and transparent to my work flow. If I could embed the skinning data in the vertices I could just reduce as necessary and bake from the vert data. Though its a nice theory that kind of stuff is a bit higher than my experience, until now I haven't had much more reason to play with baking vertex colors other than pre-lighting. If you know of a tutorial on the subject that would be extremely appreciated.
Hmm, a substitute geometry feature? I wonder when they threw that in there. Though I'm not surprised it could have possibly been that easy. I haven't done a refresher on my rigging process since 6.5 and I'm still using adapted techniques from the Digital Tutors kits. Though I do remember something about that coming up when I updated I probably didn't look into it because I didn't have a project in queue to test it out on.
As far as changing my work flow, I'm up for suggestions because I've been hitting this snag in the pipeline more and more as I work on game content and its something I need to change. If you have any ideas I'm more than willing to hear them, I'll be the fool if I stick with this method and not listen =3