I think you've got some good points in there guys...
A few approaches present themselves:
1. As monolith points out, learn the file structures for 'picking and choosing' the changes to incorporate into a "personal" supermod. The upside is that it's customized for a particular taste in play, and the performance level of one's system. The downside is that this approach wouldn't be too suitable for new comers to the sim and would generate a lot of "how do I" type questions. (See number 3)
2. Find other modders who wish to co-operate as a group and focus on making sure that their individual mods work in concert with one another. This approach would take more in the way of structure and open co-operation, but could yield some awesome results and fewer compatibility issues.
3. Create a comprehensive "How-To" for prospective modders, something perhaps like a wiki or FAQ. There is a lot of experience in these forum threads and I would think that anyone who wished to do some modding would benefit from such a work. It would also keep down the "noise" of the "how do I" posts if one could point to the resource and say "read this".
Just a few ideas...