It isn't too hard to figure out that a lot of people don't like change. Website redesigns, different music styles from a band you like, moving to a new place -- you get the point. When judging something new -- from a previous iteration of a product -- people try to compare it to it's old self, rather than something completely new and of it's own merits. So it would usually baffle me when someone would complain when something gets stale, because that is what happens when things don't change.
I've been seeing this freak out about change, in much more recent examples of Free! and Aku no Hana. Main reason for the backlash of Free! is quite simple, this anime is aim at a demographic that isn't the usual, teenage male category; it is for -- at least from the preview I've seen -- their females audience, more specifically the fujoshi. And Aku no Hana has a different art style that not many are fond of, but I'm not bothered by it and am enjoying the anime.
Still Familiar
When people want something different from the usual content, they most likely want it to be different, but familiar enough to not feel completely foreign. People tend to judge things in comparison to something similar, and when they can't do that, it is mostly described as something "strange" or "you have to see it in order to get it", which isn't convincing to many.
As a result, companies have to iterate -- rather than innovate -- because that is what is guaranteed to make money, and a lot of people do flock to these kind of things, like moe and/or romance comedy. As for the ones that innovate, they end up being cult classics and people are scratching their head asking, "why don't they make more like this?", but the simple answer is, the money isn't there for these kinds of advances.
Looking Back
Big sweeping differences don't come too often in anime, but if we were to go back to older anime -- in this case I'm using Yu Yu Hakusho as the example -- you can see a clear difference in art style. Yu Yu Hakusho's main characters don't stand out as much, compared to ones in modern anime. The characters are more realistic if anything, however less detailed in terms of animation quality.
Of course, the main reason for it being that way is because of the advancements in technology. Animators have the ability to do much more in the same amount of time it took a few years ago, or a decade in Yu Yu Hakusho's case. Eventually the quality catches up with the technology and we get better looking anime. However, if companies stayed the same, despite those advancements, would this space become too stale to continue to succeed?
Don't Stop
Of course different isn't alway going to result in greatness, but the fact that an industry is pushing some boundaries is still good, in its own right. Sometimes you need to start small, and work your way up, in order to get the audience to warm up to some new ideas. And sometimes people feel strongly enough about an idea, and just go big. What ever path is chosen -- or anything in between -- there may be initial push back, but it usually settles down in a few weeks.