Have you ever heard of the uncanny valley effect? Allow me to show you the definition before I explain further.

In aesthetics, the uncanny valley is a hypothesized relationship between the degree of an object's resemblance to a human being and the emotional response to such an object.

Now lets begin with the toy robot stage, as the industrial robot phase wouldn't help me get my point across.

Let generation 3-5 resemble the toy robot stage. 2D is a lot less creepier in these generations because we can use our imagination to fill in the gap between reality, and the little town shown on the screen.

2D is generally okay because we know that houses wouldn't be as small as 15 children, and we know real cities would have cars, and our imaginations fill in that gap between reality, and the virtual world as we think of what the towns, and cities would look like if they were shown in real life or in the anime.

3D is not okay in pokemon due to how souless it is, as our imaginations can't fill in the void between reality, and the virtual world. For an example, why is dialga, the lord of time, and space the size of a child? Why do all the houses look the same? Why are all of those somewhat realistic 3D people either moving in only 4 directions, or staying in one place? Don't they have places to be?

The fact that the people in 3D are acting as if they are 2d is generally creepy. In 2D, it was okay for people to move in only 4 directions due to only giving me the luxury of 4 directions on the D-pad. But in the 3D world, where I can move in all 360 degree angles, shouldn't the people in the 3D world act the same way?

Also, if you knew big pokemon were going to take up a lot of the screen in 3D, why go 3D in the first place? Having wailord, the biggest pokemon I know be the size of a child is unsettling, causing an uncanny valley effect that you want to avoid, hence why 2D is a better option for pokemon games.

This is why pokemon should get the megaman 9 treatment.