tech stuff:
All the action is shown in a tilted camera angle (like Alien Syndrome or Neo Contra, again). Don't know, if the player should be able to rotate the camera (depends on the control scheme - see below). The upper screen is the screen the action takes place. The touchscreen is for control and for weapon selection and other stuff.
I suggest to break the stage graphics down to detailed tile sets (see below) or object blocks and not build the stage entirely as one big chunk. If possible it would be good to do some lighting for the stage. Vertex colors will do well. It's easy to do a radiosity lighting for a stage in a 3D-application. This will add a lot of graphical quality.
Enemies could have bone animation (according to the restrictions for the DS). Textureanimation in some way is a must (for effects and other things).