Ok, let's have a think.
encoder - 2
One of these needs to be a hardware interrupt pin, so that's either pin 2 or 3 on the '328. The other can be any old digital pin, but can't be made part of a key matrix because the 2 encoder pins share a common pin, normally that's grounded. Perhaps pin 4, to keep the other hardware interrupt pin available for future use.
4x4 keypad - 8
This is the big pin-hog in the circuit. I would suggest an I/o extender. These connect to either the i2c or SPI bus. As the radio module also uses SPI, the I/o extender could share 3 of the same pins, so would only need one more pin for its exclusive use, as it's chip select pin, perhaps pin 9. MCP23S08 could do that. If you went for i2c bus, MCP23008 or PCF8574 would suit and would use pins A4, A5.
radio module - 5
This will need to be the HW SPI pins MISO, MOSI, SCK, SS, which are pins 10 to 13. Plus one other digital pin, e.g. pin 8.
a/d inputs - 2
Obviously those need to be analog pins. I would avoid using A3, A4 as you might want to use i2c bus. So let's assume A0, A1.
hw serial - 2
This has to be pins 0, 1.
direct input (Estop etc) - 2
Are these buttons or signal inputs from something? If buttons, they can potentially be made part of the keypad matrix, extending it to 5x4, which would only require one more pin. If digital signal inputs, where are the signals from and frequency/duration? Do they need to be interrupt pins, ordinary digital pins or could they be pins on an I/o extender?
So I think an 8-bit I/o extender would be my suggestion, dedicated to the keypad. This would leave you with a few spare pins on the '328 (3, 5-7, A3, at least). For future expansion you can add more I/o expander chips, with 8 or 16 I/o pins.
Finally, are you using an external crystal with the '328? If you don't need the 16MHz speed (few projects actually do) then you may be able to use the internal 8MHz oscillator, freeing up 2 pins which can be used as digital I/o pins.