Excellent question.
As has been mentioned on this site on several occasions, Host is in the process of developing a new line of controllers. That effort is huge, but is coming nicely. One aspect of that controller is the ability to do a much better job of integration with intelligent modules. With that in mind, we backed off a bit in the CTRIO2, not really sure how we'd want the CTRIO2 to play with the new CPU.
After some discussion, we decided that rather than try to make the CTRIO2 play well with the new controller, it might make better sense to split high speed counting/timing functions and motion functions into 2 separate modules. That would enable us to purify the approach to each function, rather than end up with hybrid that doesn't do either very well. So, the long term plan is to do that. The down side is that those new modules will only work on the new controllers...but you won't mind...trust me.

Now, we are rapidly approaching a point where the existing CTRIO may start facing parts obsolescence issues. Many of the chip vendors have accelerated the life cycles of some chips to streamline their operations due to the hard economic times. So in the last few days we have started discussing the possibility releasing a CTRIO-1 (rather than CTRIO2) that would be a drop in replacement for the CTRIO. It would use newer technology though, and performance would be significantly better.
Module scan times would be ~250us regardless of what the module is doing. Inputs would go to 1MHz and would be completely hardware based, meaning it would have almost none of the input limitations that the current module has. Outputs are a little harder, though. We could go very fast (perhaps even 1Mhz, although with a dither)...but...in an effort to be compatible with the existing module, we might have to limit the max output rate to 65535Hz per channel, due to the frequency variable being a WORD. I have kicked around the possibility of adding a 1X, 2X, and 4X output configuration option that would allow higher freqs with the existing data, or maybe using a new profile type to drive the higher speed. Not real sure, but we're willing to entertain any option that allows the module to be a replacement for existing CTRIO.
I would welcome thoughts on this because this is something that we may crank up shortly. Ya'll tell me what would give you the most bang for the buck.