All your points are spot on, but I think the most vital thing (and often most neglected thing) is original/intriguing/fleshed out characters. Heroes, villains, secondary characters, dead people, all of them.
Anime is one of the few mediums that can pass by with average characters... but it's the characters that usually separate the best from the bullshit (think of how many villains are just evil for the sake of being evil and heroes that are good for the sake of being good).
And when you think about it, everything comes down to the characters.
PLOT just represents what characters want and why. When what they want collides with what someone else wants, we're given conflict. When a characters succeeds or fails we're given resolution (although 75% of anime fails at this).
So to sum it up:
1. Originality/Creativity -- in all aspects (characters, plot, setting, etc). However, it needs to blend the familiar with the original... otherwise it becomes alienating.
2. Characters -- especially villains.
a) Plot -- fleshed out heroes and villains to drive the plot.
b) Setting -- needs to effect the characters, otherwise what's the point? The Matrix wouldn't work in the middle ages now would it?
3. Theme -- what the story is about. Like Anvica said,
entertainment as well as education.
4. Tone -- it's a fine art to go from comedy to super serious in the blink of an eye. Even if it is a dark comedy.
5. Everything needs to work together and serve a purpose -- fillers need to be punishable by death.
Although superficial, since anime is a visual medium, high production value is a must. I personally struggle to watch anime older than 5-10 years... pathetic, I know