This is an interesting learning project. I don't have much interest in it as a product though. The reason for that is that I (like many people) don't see much of an advantage in having two tightly coupled AVR cores. Honestly, "tightly coupled" might be stretching it. SPI would be plenty fast (simply design the protocol between them to take advantage of the duplex nature of the interface). It forces you to have a master processor and a slave. UART would be quite fast too and it allows for a symmetric connection (which I'd like in something like this were I doing it). It's really going to be a bear to program though. Unless you do something fancy, it'll need two USB connection during development.
Having said that though, I often design "multi-processor" systems. I have a robot that is going to use a raspberry pi as the main controller, an ARM as a communication hub, another as a sensor processor, each of the motors has a separate motor controller with a processor, etc. In the end, it will have over ten different processor cores. Where this differs from the Dual ATMega2560 idea, however, is that each of these processors is dedicated to a specific task. the motor controllers have a processor that focuses on controlling the PWM; temperature, voltage and current feedback signals; quadrature encoder feedback; and so forth. By splitting the design into separate processors, the design can be built up one section at a time. It can be designed, built, coded and debugged without having any affect on any other part. For personal projects, I like this process.
So I guess I'm on the side of "this is a great learning project but not something I see as making a good product." Multiple processors will always be more expensive than one large processor. There are some advantages that I see however. It will be 5v compatible. It would give an interesting board to test inter-processor communication. It could be leveraged in a true main-/co-processor arrangement. Good luck with the project! Sounds like fun!
Cheers,
Martin Jay McKee