Anyone assembling a kit would probably have or need a good pair of wire clippers, so cutting the ICSP pins shouldn’t be a problem. The header isn’t even available on a Pro Micro, so loosing it wouldn’t be a problem. Since you mention that one goal of the kit is for learning how to solder, optionally learning how to de-solder the header could also be offered in the instructions, for those wanting a bit more of a challenge.
Regardless of the “ugliness” of visible pins (a matter of opinion), I’d still rather use the Genuino Micro if it offers a better chance for full software compatibility. It would be a disappointment for some to discover that they can’t just load up a game and have it work without having to make some modifications to the code. Sketches could be written to work on both platforms but it may take extra effort, and developers would need to have both platforms available for proper testing. Besides, there are soldered pins visible on the display module, which look equally not very pretty (again, a matter of opinion).
[quote=“davidperrenoud, post:3, topic:313”]
An RGB LED is a nice idea, as it is cheap and people love playing with them.[/quote]
If the Kickstarter Arduboy includes an RGB LED, which is currently almost certain, then you should too, again for software compatibility. Some sketches may rely on it.
Not including dropping resistors and running a low PWM would mean software incompatibility. Also, running Kickstarter version code, or a programming error could cause high current to flow though an LED, possibly causing damage to it or the processor.
Maybe through-hole resistors could be placed on the bottom side, along side the Arduino board, with their leads hidden by the display.
Another thing to consider:
If you plan to use an inexpensive display module to keep costs down, it may not be 5V tolerant (many of those that claim to be 5V tolerant really aren’t), so you might need to add level shifting logic, either using discreet components or a module. The nice thing about using a Genuino Micro is that it can provide the 3.3V required by such displays and level shifters.