Most games suffer from bad planning, most projects in general suffer from bad planning. A large part of it is because of scope creep where additional ideas or features are added in to the project during development. The other reason is that the idea they have in mind is significantly more ambitious than they realized.
The Story is honestly not an issue. That is arguably the easier thing to develop for a 2D game. The breeding sections and monster selection are where problems are run into as it is exponential growth.
3D has an easier time with the monster breeding section (reference Breeders of Nyphiem) because once you get the base animations down adding more creatures becomes realitively straight forward. You need to design base models have a "mutation system" (normally minor cosmetic changes) and then set which animations it should use. If you allow rendering on system then that is it. If you pre-render then you get to the same issues as 2D. Here the story scenes are harder because you likely have to actually render plan and render them. You could get away with using idle posses but at that point you are just wasting your immersion, unless it is just a dialog.
