I would think the reason was that Samurott was the one time they might have closed an eye for the bipedal.
Or if it fought with its horn instead of awkwardly balancing on 3 legs, it could still keep its place with the Gen V starters of "no-legs", "two-legs", and "four-legs". But then that would edge into the Musketeer deers' shtick, so Samurott has to settle for looking like it's digging for seashells on the beach.>b-but the iaijitsu
If that was indeed the concept they were shooting for, it was so terribly executed it might as well not exist as part of the design. The visuals don't exist; its limbs are stout but have no sense of agility to them. A raised neck with a short tail would convey to most people that it puts a lot of its balance on its forelegs to maintain that posture instead of holding a sword up with one of them. Dewott did it well enough, I don't see why they had to toss out the entire concept and rework Samurott's body shape.
In any case, if its sprite spared a few frames in its animation for it to go bipedal for a moment, its perception might still be salvageable. But for a whole generation people basically saw it being 4-legged.