I enjoyed it just because it's more GitS, although it's nowhere near the level of SAC. I didn't like that it used the the virus angle again, but I'm not sure what was confusing about it. The plot, at least to me, was pretty simplistic.
Anime is not really popular in the USA. It's obviously popular among a niche fanbase, but it doesn't have mainstream appeal. It's actually pretty much a niche in Japan as well, save for a few popular series. It costs a great deal of money to produce a series, and the typical goal, except for original works, is not just to sell the series well (sometimes this doesn't even really factor into it at all), but to increase interest in all of the tie-in media and merchandise (manga, light novels, models, figurines, drama cds, etc.). In order to be successful, the Japanese charge extremely high prices for much fewer episodes than we would pay for here.
US anime companies can survive precisely because they don't have to pay all of the initial production costs, and they still get burnt quite often when a title they license because they think it will sell well here doesn't. Of course, there are some series that do extremely well. Eva, for instance, always has and always will sell really well here. But those types of series are really the exception.
As far as anime not always starting at the beginning or having a definitive ending/resolution, that's because the shows are generally adaptations of existing properties (light novel, visual novel, manga, etc.) that are still on-going so they don't want to hurt sales of the other types of media by having a definite resolution.
Another thing about anime is that one of the reasons it can appealing is the fact that it's made by people with a different cultural viewpoint than us, so can have different ideas and themes than we are used to coming across in everyday life.
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