John;
I will chime in with some of my ideas here. You have heard some of this, from me, before, but perhaps some of the others members will give their opinions too.
1) "Would you want the tray to be anodized or powder coated?"
The tray itself should be mill finish aluminum. Any anodized, painted or powder coated finish will quickly wear off. Aluminum is soft and none of these finishes will last in high wear areas like the top and edges of the flat bed, and on top of racks. I think a spray on bed liner such as Rhino-Liner or Line-X may be worth investigating though. The surfaces that don't get much wear, such as the exterior of storage boxes, doors and exterior of fold down side and rear panels would look best powder coated to match the vehicle.
2) "I'm undecided whether to go with a fiberglass canopy or an aluminum frame and skin canopy. Perhaps even some sort of honeycomb composite material? Any suggestions?"
I think that since you will need a variety of sizes in small quatites that molded fiberglass would not make economic sense. Aluminum frame and skin is very labour intensive but works well when custom shapes and sizes are required. Composite panels would be the easiest to customize because all the corner extrusions, edges and trim would be the same for each canopy you just cut the panels to different sizes. The last 2 pictures show a canopy on a similar tray, is this the concept you had in mind?
3) Overall Design/Market Share:
I think to appeal to the largest number of customers you need to move away from the "industrial" look and do everything you can to make the product blend in as seamlessly as possible with the truck. The first attached photo shows the typical "industrial" look, with exposed suspension, exhaust and clutter. Most of this can be accomplished by installing storage boxes and illiminating exposed rails, braces etc. The choice of hinges, handles and hardware is also very important. The second photo shows a less industrial look tray. The third pic shows a great example of an intergrated tray design, it is hard to tell where the camper ends and were the tray begins.
Cheers
Mark
on edit: Sorry I still can't seem to attach pictures, I will try again later