2D games are by their very nature, in this current generation of consoles, developed on lower budgets due to their relative technical simplicity. This leads developers to make games that rely less on massive commercial success, giving them more margin when it comes to creativity.
The 2d medium itself starts as a blank canvas, whereas in 3D a basic foundation must exist to some extent which must then be modified or built upon significantly to separate it completely from another 3D title which was created upon similar if not identical foundations.
It’s easier on a technical basis to create a unique visual style for a 2D game than for a 3D one. By default most 3D rendering engines will give you the same shading and lighting; only by adding code will you be able to end up with your own particular shaders, lighting algorithms, cameras, etc. In 2D, you have no graphical base to start from other than a limitless color palette, so it’s more likely to lead to a variety of visual styles since none are derived from a common foundation; everything is created from scratch.
A 3D character is likely to use an existing bone system to be animated, and while a proprietary and independent systems could be created it is a less enticing alternative due to the technical challenges and lengthening of development time. Yet in 2D, the proportions of a character is irrelevant as no system is widely used across the game industry to facilitate 2D character animation. Physical properties and their interactions are also completely irrelevant in a 2D system where such properties simply don’t exist by default; there is no significant challenge in having a sphere transform into a pyramid in the 2D medium, while it can be quite a monumental task in a 3D real-time engine as an underlying system of geometry dictates how objects can be displayed or transformed which has to be significantly customized to achieve anything that it was not specifically designed for. In the case of 2D visuals, it is in general just a question of drawing each frames.
These are but a few examples, yet I hope that this will help you see the challenges that developers face when it comes to creating a unique visual identity for their 3D titles, especially when the subject or genre is decided by another party. As the production pipeline becomes more flexible, developers of 3D games will have more time to dedicate themselves to unique visual representations, but it will never be as flexible as the 2D medium.