it seems to me like it would be the motherboard, but since its nintendo its the screen. all of the ds's do the same thing when a screen is faulty or loosely connected
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=== Update (03/05/2017) ===
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!confirmed! it is the lcd screen that causes the fading blue light on the wii u game pad i just did a repair on one with the exact problems listed. i attempted a battery and motherboard swap, but i did thescreen swap and bam fixed it.
it seems to me like it would be the motherboard, but since its nintendo its the screen. all of the ds's do the same thing when a screen is faulty or loosely connected