This post refers to the RCM3000 but may also be applicable to other modules.
It would be nice if the input capture channels could be programmed to operate in a counting mode rather than a timing mode. Using the start and/or stop conditions to clock the counter instead of clocking from the output of timer A8, and generating an interrupt when the counter rolled over. There are unused bits in the Input Capture Control Register, with the addition of a few more gates much higher count rates could be achieved and no more missed pulses.
Also, I wish there was at least one more quadrature decoder channel.