In other words, file systems are an excellent way to organise information. I mean, yeah - we've been using them forever.
File systems are not a good abstraction mechanism for remote procedure calls, though. I think it's important to distinguish between the two, since I find there are a lot of articles conflating both - comparing MCPs to SKILLs, which are completely different things.
I think the confusion comes from the fact that MCP came before SKILLs, and there's a mental model where SKILLs are somehow "better than" MCPs. This is like saying local Word documents are better than a fully integrated collaborative office suite. It's just not the same thing.
The reason SKILLs work so well is because there's 50 years of accumulated knowledge of how to run rudimentary Unix tools.
the TLDR
File systems - organising information MCP/APIs - remote procedure calls