The Wing Early box has a Ver.Ka style, while the Wing Zero Custom box goes with a standard MG style.
Maybe because the Wing Zero Custom is pricier and bulkier, its box is a bit bigger too.

The body is basically almost completely identical. Only the color combination is different.

The backpack and wings, of course, are completely different.

The body is all the same, except for just one part — the decoration on the outer forearm is slightly different.
Interestingly, the Wing Zero Custom has white hands, putting it in the white-hand category.

The sheer volume of the Wing Zero Custom's wings is overwhelming.

Wings open!

The difference in weapons. Looking at just the individual equipment, the Wing Zero Custom seems a bit lacking, but the wings more than make up for it.

Even though they're clearly the same body, the different color schemes make them feel like completely different kits.
There's no doubt that both are top-quality MGs, each with their own distinct personality.