One more difference I know of:
Half PWM frequencies
D3, D9, D10, D11: 245 Hz (490 Hz on UNO or 16MHz Mini)
D5, D6: 490 Hz (980 Hz on UNO or 16MHz Mini)
This may or may not bother you (most likely not). 
I use 3.3v pro minis pretty often with 3.7 Volt Li-Ion batteries - never had any issues.