I will be trying to capture a stream of 128 bits at aprox 40uS intervals. I know I can do this easily with counter/timer interrupts, although the interrupt latency could introduce some jitter, but I'm thinking of using the USART in SPI mode. The application has to do some time-consuming pattern comparisons, and I rather like the idea of no variable latency and having the hardware do the de-serialization.
I don't know if anyone's done this before, I guess I'll have to waste a GPIO or two on clock and TX, but it's a Mega2560, and I have oodles of GPIO...