Honestly, the problem with indie games using the anime style is that it doesn't feel genuine.
Some devs try to copy the "feel" of the anime artstyle, but aesthetics-wise it's closer to a stupid CalArts cartoon.
And while some can get the artstyle right, it's usually on the writing that 99% of these games fall flat.
It's especially annoying when you actually play one of these games and the writing doesn't match up with the visuals shown. In those cases there's no reason to use anime, but they still do.
Ultimately, I guess it comes down to things feeling more "western" even though they're aping a "eastern" style.