I am working on a model train set, and many years ago I started using an 80c451 to do all the controlling and sensing.
I want it to be autonomous, but don't want to program EPROMS,
But you'll still have to program your Arduino! There's no way round that, but I assure you it's quite painless.
It is looking like the Arduino Mega 2560 is perfect, (built in uP, Flash, lots of I/O) and coupled with the WiFi Shield looks like it is just up my alley.
What do you need WiFi for? Model trains can be easily controlled by an Arduino without it. You'd be better off investigating motor shields. These can control both the speed and the direction of your locos and some have servo outputs to allow you to change points.