user1335: I'd like to know the differences between these two boards: Arduino Pro Mini and Arduino Pro Micro.
Even if I've read this and this related post, it is not clear enough. I've always used the Arduino Uno or Leonardo and I'm a little bit scared of using these compact miniaturised boards.
I have seen so far those differences:

The Micro doesn’t need the separate FTDI, while the Mini does
The Micro takes more time to boot up due to USB device (keyboard/mouse) emulation (is more like a Leonardo than an Uno)
They both have 5 V and 3.3 V versions
The Mini has 2 more digital IO and 2 more analog Inputs (1 more PWM)
The pinout is the same (a shield designed for the Pro Mini is OK also with Pro Micro)
Micro is more expensive (IF you don't have already an FTDI cable).

So, what I care about most is the boot up time (because it could make debug harder) but other than that.. if I don't need the 2 more Digital IO and the 2 more Analog Inputs.. why buy one over the other?
And some more question: can I use the Mini boot loader inside the Micro to avoid the boot up time (if I do not need the keyboard/mouse emulation)?
Is the power consumption the same? Can I use the same battery?
Sorry if this is a silly question but I'm little bit confused.

user19409: Arduino Pro Mini

Pin Mapping
Arduino Micro

Pin Mapping

The Arduino page for the Arduino Pro Mini and the Arduino Micro.
Microcontroller
Arduino Pro Mini: ATmega328 (ATmega168 on older boards)
Arduino Micro: ATmega32U4  
Memory
Both have 32KB of Flash and 1KB of EEPROM
The Arduino Pro Mini has 2KB of SRAM where as the Arduino Micro has 2.5KB  
Digital I/O
The Arduino Pro Mini has 14 (of which 6 provide PWM output)
The Arduino Micro has 14 also (of which 7 provide PWM output)
Some of the analog pins can also be used as digital I/O  
Analog Inputs
Arduino Pro Mini: 8 (some boards only break out 6 analog inputs)
Arduino Micro: 12 (6 dedicated and 6 from digital I/O pins)  
USB
Arduino Pro Mini: Requires FTDI cable or Sparkfun breakout board to provide USB power and communication to the board.
Arduino Micro: Native USB  
Clock
Both are 16 MHz (although the 3V Arduino Pros run at 8MHz)
Power
There are two version of each of the Arduinos. One runs at 3.3V and 8 MHz, the other at 5V and 16 MHz.
Arduino Pro Mini: VRAW  can accept voltage up to 12VDC.
Arduino Micro: USB or external supply of 6 to 20 volts (recommended range is 7 to 12 volts)  
Interrupts
Arduino Pro Mini: The Atmega328 has 2 hardware interrupts available
Arduino Micro: The ATMega32u4 has 5 hardware interrupts available
credit: Enric Blanco 

user1566: It is more the differences between ATMega328P + FTDI (Pro Mini) vs ATMega32u4 (Pro Micro)
Apart from the minor pin differences, the peripherals for both MCUs are the same. The major difference is the ATMega32u4 has built in full-speed USB. This allows the board to function as a USB device by implementing the appropriate USB stack. E.g. it can act as a

USB to serial converter (CDC device)
Keyboard or mouse (HID device)
USB hard drive (MSC device)
MIDI controller
and more...

The LUFA library from AVR devices can be used for this but means going outside of the Arduino IDE and compiling proper C code using the latest avr-gcc tools. 
The Arduino core library has built-in support for the HID and CDC device profiles. The CDC profile is used for comms with the Leonardo, Micro, etc. while the HID profile is used for keyboard / mouse emulation.
The Leonardo / Micro boot loader implements a CDC profile for communications with the PC. This CDC profile uses Arduino vendor and product ids so unlike FTDI devices, requires an extra step to install an *.inf file on Windows. 
You would have to recompile the Pro Mini bootloader for the Micro, but even then it would require an FTDI board as programming would need to be done via the TX and RX UART pins. If you we going to go to all that trouble you could just recompile the proper boot loader to have a shorter time out. Why is difference of 1 or 2 seconds in boot loader time important?
The ATMega32u4 uses more power than the ATMega328P.

1335: <p>I'd like to know the differences between these two boards: <a href="https://www.sparkfun.com/products/11113" rel="noreferrer">Arduino Pro Mini</a> and <a href="https://www.sparkfun.com/products/12640" rel="noreferrer">Arduino Pro Micro</a>.</p>

<p>Even if I've read <a href="https://electronics.stackexchange.com/questions/96805/how-to-program-arduino-nano-pro-mini-pro-micro-clone-that-has-no-usb-port">this</a> and <a href="https://www.sparkfun.com/arduino_guide" rel="noreferrer">this</a> related post, it is not clear enough. I've always used the Arduino Uno or Leonardo and I'm a little bit scared of using these compact miniaturised boards.</p>

<p>I have seen so far those differences:</p>

<ul>
<li>The Micro doesn’t need the separate FTDI, while the Mini does</li>
<li>The Micro takes more time to boot up due to USB device (keyboard/mouse) emulation (is more like a Leonardo than an Uno)</li>
<li>They both have 5 V and 3.3 V versions</li>
<li>The Mini has 2 more digital IO and 2 more analog Inputs (1 more PWM)</li>
<li>The pinout is the same (a shield designed for the Pro Mini is OK also with Pro Micro)</li>
<li>Micro is more expensive (IF you don't have already an FTDI cable).</li>
</ul>

<p>So, what I care about most is the boot up time (because it could make debug harder) but other than that.. if I don't need the 2 more Digital IO and the 2 more Analog Inputs.. why buy one over the other?</p>

<p>And some more question: can I use the Mini boot loader inside the Micro to avoid the boot up time (if I do not need the keyboard/mouse emulation)?</p>

<p>Is the power consumption the same? Can I use the same battery?</p>

<p>Sorry if this is a silly question but I'm little bit confused.</p>
 19409: <p>Arduino Pro Mini<br>
<a href="https://i.stack.imgur.com/LKcvq.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/LKcvq.jpg" alt="Arduino Pro Mini"></a><br>
<a href="https://cdn.sparkfun.com/datasheets/Dev/Arduino/Boards/ProMini16MHzv1.pdf" rel="nofollow noreferrer">Pin Mapping</a></p>

<p>Arduino Micro<br>
<a href="https://i.stack.imgur.com/l4hOF.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/l4hOF.jpg" alt="Arduino Micro"></a><br>
<a href="https://www.arduino.cc/en/Hacking/PinMapping32u4" rel="nofollow noreferrer">Pin Mapping</a><br>
<a href="https://i.stack.imgur.com/IbHDG.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/IbHDG.png" alt="ArduinoMicro_Pinout3.png"></a></p>

<p>The Arduino page for the <a href="https://store.arduino.cc/usa/arduino-pro-mini" rel="nofollow noreferrer">Arduino Pro Mini</a> and the <a href="https://store.arduino.cc/usa/arduino-micro" rel="nofollow noreferrer">Arduino Micro</a>.</p>

<p><strong>Microcontroller</strong><br>
Arduino Pro Mini: ATmega328 (ATmega168 on older boards)<br>
Arduino Micro: ATmega32U4  </p>

<p><strong>Memory</strong><br>
Both have 32KB of Flash and 1KB of EEPROM<br>
The Arduino Pro Mini has 2KB of SRAM where as the Arduino Micro has 2.5KB  </p>

<p><strong>Digital I/O</strong><br>
The Arduino Pro Mini has 14 (of which 6 provide PWM output)<br>
The Arduino Micro has 14 also (of which 7 provide PWM output)<br>
Some of the analog pins can also be used as digital I/O  </p>

<p><strong>Analog Inputs</strong><br>
Arduino Pro Mini: 8 (some boards only break out 6 analog inputs)<br>
Arduino Micro: 12 (<a href="https://www.arduino.cc/en/uploads/Main/ArduinoMicro_Pinout3.png" rel="nofollow noreferrer">6 dedicated and 6 from digital I/O pins</a>)  </p>

<p><strong>USB</strong><br>
Arduino Pro Mini: Requires FTDI cable or Sparkfun breakout board to provide USB power and communication to the board.<br>
Arduino Micro: Native USB  </p>

<p><strong>Clock</strong><br>
Both are 16 MHz (although the 3V Arduino Pros run at 8MHz)</p>

<p><strong>Power</strong><br>
There are two version of each of the Arduinos. One runs at 3.3V and 8 MHz, the other at 5V and 16 MHz.
Arduino Pro Mini: VRAW  can accept voltage up to 12VDC.<br>
Arduino Micro: USB or external supply of 6 to 20 volts (recommended range is 7 to 12 volts)  </p>

<p><strong>Interrupts</strong><br>
Arduino Pro Mini: The Atmega328 has 2 hardware interrupts available
Arduino Micro: The ATMega32u4 has 5 hardware interrupts available<br>
credit: <a href="https://arduino.stackexchange.com/a/34577/19409">Enric Blanco</a> </p>
 1566: <p>It is more the differences between ATMega328P + FTDI (Pro Mini) vs ATMega32u4 (Pro Micro)</p>

<p>Apart from the minor pin differences, the peripherals for both MCUs are the same. The major difference is the ATMega32u4 has built in full-speed USB. This allows the board to function as a USB device by implementing the appropriate USB stack. E.g. it can act as a</p>

<ul>
<li>USB to serial converter (CDC device)</li>
<li>Keyboard or mouse (HID device)</li>
<li>USB hard drive (MSC device)</li>
<li>MIDI controller</li>
<li>and more...</li>
</ul>

<p>The LUFA library from AVR devices can be used for this but means going outside of the Arduino IDE and compiling proper C code using the latest avr-gcc tools. </p>

<p>The Arduino core library has built-in support for the HID and CDC device profiles. The CDC profile is used for comms with the Leonardo, Micro, etc. while the HID profile is used for keyboard / mouse emulation.</p>

<p>The Leonardo / Micro boot loader implements a CDC profile for communications with the PC. This CDC profile uses Arduino vendor and product ids so unlike FTDI devices, requires an extra step to install an <code>*.inf</code> file on Windows. </p>

<p>You would have to recompile the Pro Mini bootloader for the Micro, but even then it would require an FTDI board as programming would need to be done via the TX and RX UART pins. If you we going to go to all that trouble you could just recompile the proper boot loader to have a shorter time out. Why is difference of 1 or 2 seconds in boot loader time important?</p>

<p>The ATMega32u4 uses more power than the ATMega328P.</p>
