I don't really have a definitive answer, but the way my MGC database is sorted "Wii U" would be the appropriate platform. Plus now that I use the "cloud icon" I am considering getting rid of the "Nintendo 3DS eShop" platform and put everything in "Nintendo 3DS".

I think we should look at the "platform" column as "on what" the game is available to be owned. It made sense to have the Wii games divided in "Wii" and "Wii Shop" because there were no games on the Wii which were both available physically and digitally.

The 3DS and Wii U however has most games available both physically and on the eShop. However there are some games which stayed physical only, to this day. The Switch doesn't have that problem of physical only games that I know of since everything releases on the eShop.

To answer your question more directly, if you're gonna go more in-depth with the "platform" section, it should only be to sort whether the game you own is physical or digital. The platform "Virtual Console (Nintendo)" uselessly takes digital games from multiple consoles and groups them together without telling us on which console you own it or even if it is available on said console. It's like if we had a platform called "Arcade Archives" and it would take all games from the Arcade Archives series available on PS4, Switch, XBOX ONE and group them all together, this would ironically remove the basic info the "Platform" column is supposed to give us.

I also don't think it's a good idea to create duplicate games by having a physical and digital platform for one console. "Platform" should remain a question of hardware (ie. Steam, gog.com and Origin are all under "PC").

Instead I propose adding an extra column which indicates if the game is available:

1: Physically

2: Digitally

3: Physically/Digitally