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Next difference - Arduino Uno R3 has ICSP pins (6 pins near onboard LED) while Netduino Plus 2 has 10 tiny holes there (next to onboard button). As far as I know, the USB Host Shield uses that. Maybe Chris can comment on this difference.
I've got similar background :-) I have both Arduino Uno R3 and Netduino Plus 2.
The main issue is that Uno has 5V I/O whereas N+2 has 3.3V I/O. In digital mode they are compatible - N+2 can stand 5V and 3.3V is HIGH on Uno. But watch out when you are using analog (especially inputs) on N+2.
For example I had this is a problem when using 16x2 LCD Shield buttons - there is one analog input for 5 buttons and each button causes some known voltage drop. When no button is pressed, there is 5V on A0. In theory you may damage N+2 this way, but some guys on this forum tried that and said N+2 can stand 5V. But still some buttons will not work.
I had similar problem when upgrading to 4.2.2.2 using DfuSe Demo v3.0.3 on Windows 7 64bit SP1. Tried both 64 and 32 bit DfuSe versions.
Download phase goes to 100% and immediately on next phase application crashes. DfuSe Demo also crashes on Verify.
Suprisingly, after such crash, detaching and attaching Netduino, NETMF detected it. I was able to change MAC address, deploy and run some simple app.