Why not use the PIC?
There are some issues with the current .NET Micro Framework implementation that limit its usage in such scenarios. I don't know exactly how the PIC drives the H-Bridge, but I can think of
1) Bit-banging - it depends on the frequency. Netduino's managed code is interpreted, i.e. slow. IIRC it can produce signal at 10 kHz range - I am not sure how fast you need to drive those power MOSFETs. Also, the code can be disturbed at any time, for example by garbage collector or interrupt handler, so the motor control will be stuck for relatively long time in certain state, which is not something you'd want. There are some techniques to minimize such events, but no guarantees.
2) Timers or PWM - there is missing the key feature: synchronized channels. The signals for left and right part of the H-Bridge must have precise relationship, they cannot overlap at certain moments etc. - usually, you configure two channels with opposite polarity, dead time and then start them at the same time. This would require firmware modification (the microcontroler has these features, but they are not accessible from managed code).
Personally, I would go with the PIC(s) - you've already got proven working (?) design, it is much better for real-time control, and also significantly cheaper. You can use Netduino to control them, if you must... 
