I believe it was more storage (probably 32gb vs 64gb) & Splatoon bundled. I wouldn't be surprised to see a few other small extras like the Joy-Con Grip & My Nintendo coins as well.
Bigger SD card, okay.
Bundled game, okay.
I assume with the Joy-con grip you mean the bridge part to make a dog face. Such a piece of plastic isn't expensive and should come with every SKU. The same goes for the My Nintendo coins.
Although the only difference between SKUs should be bundled games and/or additional controllers (as in, a Pro Controller), that way the lower priced standard SKU won't feel gimped. Better not repeat that Wii U nonsense.