As far as I know, no one has found any documentation of why any particular letter was skipped or used. Always seemed odd to me that "C" was skipped over then used 8 years later. Going down the path that Gary started, you will find more letters were used than it initially looks like. They weren't necessarily models, but may have been used as modifiers. Given the time frame for some of these, there was probably less of a master plan than this makes it look like.
Beyond the well-known tractor models:
D - Diesel (example MD)
F - pre-1939 models (F-20)
I - "International" (I-4)
L - "Lo-Boy", spelled out in tractor names but used on implements (L-22 mower)
N - narrow tread (BN)
O - "Orchard" (O-4)
P - "Power unit" (P-12)
R - "Rice" (WDR-9)
S - "Special" (OS-4)
T - "TracTracTor" (T-20)
U - "Power Unit" (U-2)
V - "Vegetable" (AV)
W - "Wheel" (W-4)
One oddity that shows up is in the serial numbers for the M. Typically you see the tractor model replicated in the serial prefix, example A with "FAA". The M uses a "K", with a prefix of "FBK". Could that be a leftover from an initial plan of calling it the model K? Did somebody decide they didn't want a double "M" in the engine prefix, as in "FBMM"? As of now, nobody knows.