Firstly, I think Final Fantasy: The Spirits Within was a poor choice of name. The Spirits Within would have been a more suitable title.

Secondly, it was well animated. The visuals were gorgeous.

Thirdly, I liked the plot mainly when it didn't feel like a riff on Aliens. It's not fair, but that movie set the benchmark for space marines versus aliens, and anything made since then along the same lines feels derivative.

Despite the flaws, I found myself liking it, but not loving it.