Im sure there are more reasons but updates to prompts and tools coming from the server side is a major one.

It's typed so you can build some governance around it, by allowing only some tools or parameters for your org (this is a pretty weak point, but still)

A skill has one giant description from the frontmatter loaded into the context, where MCP loads a smaller one for every tool. Not necessarily better, the skill approach is often better actually, but sometimes the MCP approach fits more