Note it's just "Spine", not "Spine 2D". 😄
Besides the aspects mentioned above like artistic style, size, rendering performance and simplicity, etc, it's important to note that 3D can be very time consuming. You postulated that 3D has faster workflows. While it depends on the project's needs, I think this is rarely true. The 3D pipeline often consists of multiple specialists, while 2D is more approachable for small teams, or even a single person. It's awesome to have a super detailed animated 3D model that you can view from any angle, but creating that takes a lot of effort. If you are doing something where you can make full use of that effort, it can make sense. Otherwise it can much easier to paint 2D detail than it is to model it all in 3D. In many cases it isn't necessary to view from any angle, so extra effort to enable that is wasted. Also, animating in 3D can require a lot more effort.
A lot of animation is about how the end result looks, not about being physically accurate. Even in 3D, animators may need to deviate from being physically accurate, similar to the "tricks" employed in 2D to achieve a particular look. Cheating perspective, exaggerating motion, and other tricks in 2D are quite easy, but in 3D that can be difficult or impossible when it needs to look correct from all angles. This gives 2D advantages across many art styles, with a handcrafted feel that can be appealing and makes for unique branding.
Even projects from top studios with huge budgets that are very 3D heavy still employ 2D for visual effects, UI, stylized sequences, promotional assets, etc.
The benefits of 2D make it a good choice for many types of projects. 3D can be amazing and has its place too, but 2D is in no danger of becoming obsolete.