I'll discuss the findings in two parts: Regional Ancestry and Deep Ancestry.
According to the website, Regional Ancestry "is based on the mutations across all your DNA and therefore shows the contribution from every one of your hundreds of ancestors." Deep Ancestry is based on the Y chromosome and mitochondrial DNA and "shows only a single line of descent."
My uncle's neanderthal percentage was calculated as 1.9% by Geno 2.0, while 23andMe figured 2.7%. Close enough.
What struck me was the population calculation: 42% northern European; 40% Mediterranean; 18% southwest Asian. 23andMe paints my uncle (and his siblings) as 100% European. (You can play with various admixture tools at GedMatch and other sites, but little DNA other than European is detected.) This may be why The Genographic Project describes its determination of Regional Ancestry as "unique."
The percentages of ancestry used to determine Regional Ancestry are compared against 43 Reference Populations. My uncle is most similar to modern-day people of Denmark and Germany. We have no known ancestry from Denmark, but the connection may pre-date records so far discovered.
You can view the ancestry percentages of the 43 reference populations. My uncle is similar to other European populations besides Danish and German.