The settings in anime tend to be very strong and do not simply provide a space for the action to take place, but instead firmly direct the action of the story. They do this by providing exceptionally dynamic environments that typically force the characters to constantly be interacting with and reacting to their physical situation. For instance, in "Trigun" the characters' actions are usually reactions to the needs and conflicts created by the apocalyptic wasteland they live in. Nearly any setting is possible for an anime, but there are some established settings that have become part of the anime canon. Science fiction anime set in space or another planet ("Cowboy Bebop," "Outlaw Star") is one well established trope, as is the "mecha" genre, which is centered around giant robots ("Gundam Wing," "Evangelion"). Other common settings are Japanese high schools, post-apocalyptic planets ("Trigun"), sword and sorcery-style fantasy worlds ("Record of Lodoss War"), Edo period Japan ("Samurai Champloo"), and the city of Tokyo past, present and future ("Akira," "Boogiepop Phantom").
Another important decision is how long your story will be and what format would best fit it. The standard choices include a one-off film, a film series, a one-season television series, a multi-season television series, a long-term television series, or a combination of these. If you want to write a closed story which wastes no time in progressing the action of the main plot, a one-off film or one-season series will work best. If you wish to write an arcing story with many subplots, a film series or multi-season series is for you. For an open-ended story which allows for easy later additions, try a long-term series in the style of "Naruto" or "Inuyasha."
Like all stories, those in anime are defined by their approach to subject matter through their mood, but within the anime medium it is a very specific issue. A useful over-simplification is to think of anime as a two-sided coin, with utterly silly comedy on one side and dead serious drama on the other. Most anime flip between these two sides, alternating but rarely blending dramatic and comedic elements, and nearly all are more focused on one than the other. Decide whether you would like your anime to be comedic, dramatic or a little of both, and then decide what balance you will strike between the two.
Mainstream anime tends to be populated by straightforward character archetypes, while the less mainstream tend to subvert archetypes. Common anime character types include the shy character who slowly learns to channel his inner strength, the wild rogue who develops into a highly moral hero, the nerd with reservoirs of emotional strength, the overly sexual klutz with a heart of gold, and the inhumanly immoral villain, among others. It is important to have a general knowledge of common anime archetypes, as they are repeated over and over again and are very well-known by anime fans. When creating characters, use these archetypes, but make sure to put your own spin on them, or your viewers will find them distasteful.