In Japan, Eva tends to be as popular as The Matrix or Star Wars. In America, Eva tends to be only slightly more popular then any other low-brow fan service-riddled monstrosity. Sure, both NGE and NTE (and almost any Eva merchandise out there) tends to have elements of sex appeal about them, Eva is not primarily about sex appeal. Just like how The Matrix or Star Wars tend to also have elements of sex appeal about them (beautiful actors in skin-tight leather in The Matrix, Princess Leia's slave outfit in Return of the Jedi), those titles aren't primarily about their sex appeal either. In both examples, sex appeal is used to a greater narrative goal of character development and world-building.
But, one couldn't really find any contradiction in selling either Star Wars or The Matrix in an environment where sex appeal is the main focus. After all, the sex appeal in both titles are fairly successful in achieving the desired effect in their respective viewers. (One Star Wars fan told Carrie Fisher that he "thought of her" at least four times a day.) It all depends on what you sell along side of those titles that will decide how the surrounding culture that shops at your store consider those titles. Now, in America, those who consider mostly only sex appeal when thinking of The Matrix to Star Wars are in a minority. Much of the culture still consider these titles to be more pop-culture icons rather than titles that feature sex appeal. But you can still find a few places that only sell merchandise of these titles that relate to their inclusion of sex appeal. (Spencer's Gifts readily comes to mind, though there may be others.)
In America, however, Eva has always been sold along side more perverted, blatantly sex-obsessed titles. A fair amount of ADV's titles contain anime where the entire focus of the story was about sex. In order to watch Eva on ADV's DVD releases, I usually find myself watching ads that feature Colorful and Mezzo Forte, which have no thematic or genre similarities to Eva's main narrative goals. Their similarities to Eva are all aesthetic, featuring sexy girls either performing in action scenes or sexy girls in various states of undress. That is what Eva is sold with in America. This is how most Americans that know of Eva also relate to Eva. The audiences are mainly aware of the sex appeal. In Japan, however, Eva isn't paired with such titles in their pop-culture environment, so the connection between such titles isn't as prominent in Japan as it is in the United States. As a result, Japanese audiences may not as readily relate Eva with strictly the aspects of sex appeal found within Eva. Eva is about more than just sexy girls, and their cultural awareness of Eva reflects that notion. Sure there's sex appeal to be had, but that isn't even the main focus of the culture's interest in Eva. They're interested in it as more of a pop-culture icon than they are a series of gratuitous fanservice scenes.
Because Eva's sex appeal is further accentuated by the more obviously risqué titles that ADV (and now Funimation) associate with it, American audiences tend to focus more on the "waifu" characters of Eva than Japanese audiences would be, thereby effecting its critical reception. This is why NTE tends to get taken down in American discussions because "Best Girl didn't get enough screen time." After all, Eva is sold in America along side of all of the other late-night Anime titles, so why shouldn't an American relate to Eva in a way that isn't evocative of late-night Anime titles? (Which have become a weird Rubix's Cube of fan service and character development of late.) So, just like many people's first thought when it comes to Star Wars is lightsabers and Jedi, and not Leia's slave outfit, many Japanese people's first thought of Eva are the Units and NERV, and not Asuka's Test Plugsuit. But the marketing and associated titles in America, however, tends to warp that perception, causing American fans to be in it more for the waifus than many Japanese audiences are. Many American's first thought when Eva is mentioned (other than "What the Hell is an Eva?") is the body of either Rei or Asuka.