I'm still in the finding out phase with the D800E but the best tonal separation and color I'm getting so far is within Capture NX2. I'm a C1 user but for some uses that may have to change. NX2's default output is more than a little better in the landscapes/architectural shots I've played with so far, especially the greens. NX2 used to be a glluttonous resource pig and I'm happy to say the latest version flies, even on a 5 year old dual core 2.5GHz laptop (granted with an SSD installed). I spent some time dialing in C1 to try and match NX2 but it's not happening yet, the R,G and B histograms reveal a significantly different default treatment.
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Debating starting a new thread but it's all about color so here goes. I'm starting to think C1 has more accurate color and NX2 more pleasing. I did some testing in late day direct sun and early afternoon shade. I'm attaching a comparison that was color managed carefully throughout (Adobe 1998), converted to sRGB for safety now, showing the unedited, default output from both programs.
There's so much more than NX2 being warmer going on. Contrast is handled better, midtones have more separation. Too bad NX2 sharpening looks like sh*t. I let C1 do that to the .tif output to keep the playing field level.
Anyone can run a file through a trial version of NX2 (60 days at this point) but if you care to try this one for yourself
it's here, at least until the bandwidth runs out.
I also want to add that I'm not advocating one over the other. All I care about 95% of the time is the fastest route to the most pleasing image. Period.