I use DxO with Lightroom. Or standalone. It has a browser, but that's about it. C1P has essentially a grafted on media organizer (I can't remember its name) with their RAW processing features, so it's apples to half apples, sort of.
The DxO workflow with LR is superb, especially the DNG option. Gives you much more control. And the standout features for me are perspective controls, lens adjustments (you only have to download the stuff for your equipment), and the haze, noise and lighting controls. It has a better de-hazer than anything else IMHO.
What happens when you use a dng to slingshot to DxO and back? LR reads the dng -- with all the changes you made in DxO? How did they manage that coding trick?
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Are you creating the structure in the catalog or in the User Collection area? This, of course, is different in that if you are creating folders in the catalog you are creating "real" folders on your hard drive and moving files. If you are creating folders and such in the user collection area it's all "virtual"...if you will.
I haven't experienced what you did but it seems Aperture did something similar if you used Smart Albums. A project would have all the files and Smart Albums would duplicate certain sets. I believe Capture 1 works the same way.
So far I'm experimenting with using just Folders and Smart Albums in the User Collection area and maintaining a single Capture 1 Catalog. It's working ok and if you are diligent with using keywords it gives you a lot of flexibility in how to create Smart Albums. I'm a little concerned with a single C1 catalog but that's how I had Aperture set up and it was fine. One thing that's a bit annoying with Smart Albums is that you can't use the Edit With function (send to NIK for example) when you are in a Smart Album. Not sure why, but you have to go to the image in the Catalog to use the Edit With function.
Two suggestions to try:
You guys might want to look into organizing by Sessions instead of Catalogs.
If you remain on Catalogs, I've heard that you can get around the speed thing by using one Catalog per shoot, as opposed to continually dumping new images into an existing Catalog so it swells in size.