>>43435975There's literally nothing wrong with its color scheme. For one the blue and pale yellow combo has been a thing since time inmemorial because Complimentary color schemes are the single most popular color schemes both for character design and scene grading. More than half of all predominantly blue Water Type pokemon have the same color combo.
Blastoise, Gyarados, Lapras, Seadra, Lanturn, Wailmer, Samurott, Feraligatr, and a lot more. If anything, this last one gets praised often, but it's actually unfittingly colored as it's aiming for a Three-Way Color split, but without Green to compliment it. Greninja on the other hand is in a perfect Split Complimentary color range, which is a less contrasty, more pleasing version of the Traditional Complimentary range. Therefore it manages to both stand out from most other Complimentary focused designs and be visually pleasing to look at. I think that's subconsciously why it's also such an enduringly popular design. It pleasingly stands out.