I assume you mean Unity's built-in 2D Animation system.

In general the Unity 2D animation system will most likely lead to equal or better performance, since its animation featureset is very limited and uses GPU skinning. This is planned in spine-unity as well (under this issue ticket), but we did not yet get to implement this feature. spine-unity will currently perform CPU skinning (a mesh is generated and rendered using a standard MeshRenderer) but supports a far larger feature set.

You can download the spine-unity runtime free of charge for performing some benchmarks and performance comparisons on your machine.
Spine Unity Download: Download

The main question is if animating and managing skins, constraints, and so on in Unity's 2D animation framework is something that you want to use as a developer or animator. Both animating and managing skins is, well, "not very mature in terms of usability" to put it mildly.

Um, the issue ticket you linked leads to 404 error. I hope it doesn't mean GPU skinning is no longer planned, because it's an amazing feature

Thanks for the hint! This issue ticket was on the internal board only and thus was not shown as broken for us.

We have created a public version of the same ticket here now and updated the url above:
https://github.com/EsotericSoftware/spine-runtimes/issues/1843