About the missing controls, there latest one I saw was someone saying something about the Mu-Tron III models (the Tron Up and Tron Down) not having the same sort of sensitivity controls as the original.  That may be true.  I guess I've not done enough with those models to be all that concerned about it.  Actually, there are a lot of the models that give you additional parameters over the vintage effects that were modeled.  There's definitely nothing I noticed that has prevented me from getting the sounds I want, though.  It's the most flexible effects unit I've ever used.

As far as the dual effects chains, it can't really be done, although you can have two separate paths through the M13 if you use it's effects loop.  You can have one path going through the M13's input and out the M13's effects send and then another going in the M13's effects return and out the M13's output.  With this though, you're still limited to a total of four effects, so you can have two effects in each path or 3 in one, 1 in the other.  The other thing to consider is that with many of the effects it is possible to bring them in and out of the chain with the expression pedal controlling the mix control.  I do this with modulation effects quite often.  But you could do it with delays, filters, and reverbs as well.  You can't really blend in a distortion, but you can control any of the distortion parameters with the expression pedal.  Overall, the expression pedal control available on the M13 far surpassed what the X3L can do.