Any specific reason to use the tiny 0402 parts?

[bootsector]

Why not just using through hole or other more hand-soldering friendly sizes?

[Ancyker]

For which PCB?

The point of decoupling capacitors is to reduce the inductance of the power/ground loop. As smaller packages tend to have lower inductance, the smallest package size should be used. There is absolutely no benefit to using a THT capacitor as a decoupling capacitor -- you can omit the capacitor entirely if that is your plan.

For instance, the capacitor on the PIC CIC module does nothing; if you omit it, it will still usually work, and if it doesn't work without it, then it likely won't work with it either. I prototyped VSELECT with THT capacitors; it didn't like it (initially, the voltage would be unstable), but it functioned. Removing the capacitors did not change anything -- the voltage was still just as unstable.

As for the RTC, here's a direct quote from the datasheet:

Power-Supply Decoupling
To achieve the best results when using the DS3231M, decouple the VCC and/or VBAT power supplies with 0.1uF and/or 1.0uF capacitors. Use a high-quality, ceramic, surface-mount capacitor if possible. Surface-mount components minimize lead inductance, which improves performance, and ceramic capacitors tend to have adequate high-frequency response for decoupling applications.
If communications during battery operation are not required, the VBAT decoupling capacitor can be omitted.

With that said, people have edited the PCB to use 0603 capacitors instead and haven't reported any issues. However, as 0402 is optimal, the project should continue to use 0402 as the default.

[bootsector]

I mean, the project is DIY friendly and already uses lots of non-state-of-the-art stuff (i.e., pin headers). I don't think switching from 0402 to anything else would make any difference on the design and how it works (as you said, everything should still work even without some of the 0402 parts).

[Ancyker]

You are partially correct.

First, as I said, if you don't want to solder SMT capacitors, then there is no difference between omitting them entirely vs using THT capacitors. For the most part, it will still work. However, the unstable voltage may reduce component lifespan. If you'd prefer to use a different size of SMT capacitor, you can just change the footprint.

Second, the new revision I'm working on adds far more (optional) SMT components -- you'll be able to install the entire ATmega2560 module, clock gen, etc, on the main PCB as well as connect to a top PCB via FPC cables. The new top PCB also adds decoupling capacitors to the cartridge slots.

[bootsector]

Oh, by looking at this new revision boards, I can see where the project is going. And yeah, people should still be able to create daughter boards with whatever easier-to-solder components on them and just connect them to the main PCB via pin-header interfaces. Thanks for taking the time for answering my question!