Arduino Uno R3 vs Arduino Mega 2560 R3

The two boards side by side, from the same board files BoardPilot uses to check your wiring.

	Arduino Uno R3	Arduino Mega 2560 R3
Chip	ATmega328P	ATmega2560
Processor	8-bit AVR ATmega328P at 16 MHz, 2 KB SRAM, 32 KB flash, 1 KB EEPROM	8-bit AVR ATmega2560 at 16 MHz, 8 KB SRAM, 256 KB flash, 4 KB EEPROM
Logic level	5 V	5 V
Header pins	29	83
GPIO pins	20	70
Analog inputs	6	16
Default I2C	SDA A4, SCL A5	SDA SDA 20, SCL SCL 21
Default SPI	MOSI ~11, MISO 12, SCK 13	MOSI 51, MISO 50, SCK 52
5 V tolerant inputs	yes	yes
Flashing tool	avrdude	avrdude
Arduino board	arduino:avr:uno	arduino:avr:mega

Which one to pick?

Pick the Arduino Mega 2560 R3 if you need more GPIO pins (70), more analog inputs (16).