Interesting stuff. When I was a messenger, the biggest problem I had was getting in and out of buildings quickly. If your system had some sort of database with instructions on every building in the city - is there a freight elevator, courier entrance, building mail room, security at front desk, after hours procedure, etc. - that would be helpful, and I'll bet every courier company would subscribe to such a service.
As for all that route planning, I think you're inventing a problem to solve it. Most messengers plot out a few safe, fast routes, a couple routes uptown and a couple downtown, and adapt those routes to their destinations. Courier companies have regular clients just like everybody else, and you find yourself going to the same addresses over and over. Nobody makes money by riding faster, or by riding fewer miles, you make money by carrying more packages. The dispatcher back in the office is the one who needs the route planning software, so he can load up his messengers with packages moving in the same direction.
Also, the most direct route is seldom the fastest or safest route by bicycle. A back road with light traffic and easily run red lights will be much faster than a direct main road with a lot of traffic and difficult intersections. You could spend years computer modeling every intersection and recommending more logical routes, but a guy on a bike will still take a left hand turn where there is a break in traffic. A road that you have ridden 100 times will be faster, for you, than a road you are riding for the first time.
Granted, I worked in two relatively logically laid out cities in the US. Things might be different in, say, London, where I understand even locals need maps to get around.
I'd say the biggest problems a bike messenger faces are communicating with the dispatcher, and getting in and out of buildings quickly.
I'll be watching your blog - looking forward to see what you come up with.