Quote - You could set up geometry switching to use the exact same geometry but with different UV maps to deal with the UV stretching.

Yes that makes a lot of sense, though discontinuity might still be a problem in animations.

Quote - Weight mapped characters would be a lot more complex to set up, and could make for some rather large cr2's as well.

If you are using the exact same geometry it would use the the same weight map. The weight map is in the cr2 not the obj, so geom switching would not cause increase in size due to the weight map.

Quote - To complicate matters even more, any injections would also have to be injected into the additional geometry as well.

Not so! If only swapping the UVs, whilst keeping the same vertex count and winding order, no extra deltas are required. Same as with the weight map, the deltas live in the cr2, not in the obj, with the same winding order and vertex count all switched geometries would use exactly the same morphs.