It would be cheaper to make, yeah, but crazy and lively animations are harder to do in 3D than 2D (Note that 2D lets you what ever the hell you want with the character, 3D doesn't have
that much freedom.)
Consider that detachable body cat girl (aka Ms Fortune). In 2D, animating her is no harder than any other character, but would be far harder in 3D.
Overall, 3D is often used for cost-cutting where 2D animation would be too expensive (see: Kirby anime), so if you want the game to really pop out, 2D is a nearly always a better idea. Of course, lively animation is possible in 3D (like our very own Smash Bros), but you can see how expensive that can get.