I had a similar question recently about generating signals from a high speed MCU where I assumed since the Arduino can generate 4Mhz square waves at 16Mhz that any MCU could generate signals at 4 instructions per. It turns out not to be true at all. 14Mhz tops on a 700Mhz Raspberry Pi:
http://codeandlife.com/2012/07/03/benchmarking-raspberry-pi-gpio-speed/
Unimpressive! 
128 channels? I am thinking FPGA too in this case, though I know not much about them other than the better ones are fast and have a lot of pins. Maybe you can have the MCU program the pattern into RAM organized as 128 bits wide and have the FPGA fetch it 128 bits at a time and bang it out over the 128 output lines. Probably you could run that a lot faster than 1Mhz and very accurately. There is a lot of 10ns SRAM available and lots of FPGAs that can run at 100Mhz or better. Have fun soldering a high-end BGA FPGA. 