Do u liek Mudkipz?

Having the mascot in reverse color confuses everyone. Like let's say Kyogre (the Ocean Legendary) is the Ruby Version Mascot and Groudon (The Land Legendary) is the Sapphire Version Mascot.

So no. Matching the colors > Mixing.

Kyogre was blue with red lines on his body, whereas Groudon was red with black lines on his body. Hell, even Rayquaza, the Emerald mascot, was green with yellow lines on his body. Reshiram and Zekrom are, as far as coverart goes, pure black and white. they would blend in too well with the background, so the contrast is the best call, both logically and aesthetically.