Since there appears to be motion on this. I'd like to add more detail. Our problem right now is almost entirely the number of files created to accommodate indexes. While one file per database might be nice for some, I'd imagine that some of the performance benefits of unique file per collection would be lost. However, I would absolutely love to be able to reduce the index files from 1 per index to 1 per collection. I'm not saying merge index file into collection file... simply allow the option to have 1 file for each collections entire set of indexes.
We average 30+ indexes per collection, so this would be huge for us.