MCP does three things conceptually: it lets you build a bridge between an agent and <something else>, it specifies a UI+API layer between the bridge and the LLM, and it formalizes the description of that bridge in a tool-calling format.
It's that UI+API layer that's the biggest pain in the ass, in my opinion. Sometimes you need it; for instance, if you wanted an agent to access your emails, a high quality MCP server that can't destroy your life through enthusiastic tool calling makes sense.
If, however, you have, say a CLI tool or simple API that's reasonably self documenting and you're willing to have it run, and/or if you need specific behavior with a different context setting, then a skill can just be a markdown file that explains what, how, why.
All public MCP server I’ve seen have been a disaster with too many tools and tokens polluting the context. It’s really most useful when you need tight integration with some other environment and can write a little custom wrapper to provide it.
People like to shit on Copilot's UX but something it does well is making it incredibly easy to switch off individual tools you don't need per MCP server. In general I've found its MCP story the best out of all of them (Codex/CC/Gemini), it utilizes VSCode extensions integration very well.
I will say, when using MCP be selective about which tools you enable. A lot of the time they come with say 30 tools and you only personally care about 5 of them. The other 25 are just rotting your context.
The durable pattern here isn't a specific file format. It's on-demand capability discovery: a small index with concise metadata so the model can find what's available, then pull details only when needed. That's a real improvement over tool calling and MCP's "preload all tools up front" approach, and it mirrors how humans work. Even as models bake more know-how into their weights, novel capabilities will always be created faster than retraining cycles. And even if context becomes unlimited, preloading everything up front remains wasteful when most of it is irrelevant to the task at hand.
So even if "Skills" gets replaced, discoverability and progressive disclosure likely survive.
The problem isn’t having a standard way for agents to branch out. The problem is that AI is the new Javascript web framework: there’s nothing wrong with frameworks, but when everyone and their son are writing a new framework and half those frameworks barely work, you end up with a buggy, fragmented ecosystem.
I get why this happens. Startups want VC money, established companies then want to appear relevant, and then software engineers and students feel pressured to prove they’re hireable. And you end up with one giant pissing contest where half the players likely see the ridiculousness of the situation but have little choice other than to join party.
Anyway: a lot of earlier stages of drug discovery involve pulling in lots of public datasets, scouring scientific literature for information related to a molecule, a protein, a disease, etc. You join that with your own data and laboratory capabilities and commercial strategy in order to spot opportunities for new drugs that you could maybe, one day, take into the clinic. This is traditionally an extremely time consuming and bias prone activity, and whole startups have gone up around trying to make it easier.
A lot of the public datasets have MCPs someone has put together around someone's REST API. (For example, a while ago Anthropic released "Claude for Life Sciences" which was just a collection of MCPs they had developed over some popular public resources like PubMed).
For those datasets that don't have open source MCPs, and for our proprietary datasets, we stand up our own MCPs which function as gateways for e.g. running SQL queries or Spark jobs against those datasets. We also include MCPs for writing and running Python scripts using popular bioinformatics libraries, etc. We bundle them with `mcpb` so they can be made into a fully configured one-click installer you can load into desktop LLM clients like Claude Desktop or LibreChat. Then our IT team can provision these fully configured tools for everyone in our organization using MDM tools like Jamf.
We manage the underlying data with classical data engineering patterns, ETL jobs, data definition catalogs, etc, and give MCP-enabled tools to our researchers as front end concierge type tools. And once they find something they like, we also have MCPs which can help transform those queries into new views, ETL scripts, etc and serve them using our non-LLM infra, or save tables, protein renderings, graphs, etc and upload them into docs or spreadsheets to be shared with their peers. Part of the reason we have set it up this way is to work through the limitations of MCPs (e.g. all responses have to go through the context window, so you can't pass large files around or trust that it's not mangling the responses). But also we do this so as to end up with repeatable/predictable data assets instead of LLM-only workflows. After the exploration is done, the idea is you use the artifact, not the LLM, to intact with it (though of course you can interact with the artifact in an LLM-assisted workflow as you iterate once again in developing a yet another derivative artifact).
Some of why this works for us is perhaps unique to the research context where the process of deciding what to do and evaluating what has already been done is a big part of daily work. But I also think there are opportunities in other areas, e.g. SRE workflows pulling logs from Kubernetes pods and comparing to Grafana metrics, saving the result as a new dashboard, and so on.
What these workflows all have in common, IMO, is that there are humans using the LLM as an aid to dive understanding, and then translating that understanding into more traditional, reliable tools. For this reason, I tend to think that the concept of autonomous "agents" is stupid, outside of a few very narrow contexts. That is to say, once you know what you want, you are generally better off with a reliable, predictable, LLM-free application, but LLMs are very useful in the prices of figuring out what you want. And MCPs are helpful there.
How do you handle versioning/updates when datasets change? Do the MCPs break or do you have some abstraction layer?
What's your hit rate on researchers actually converting LLM explorations into permanent artifacts vs just using it as a one-off?
Makes sense for research workflows. Do you think this pattern (LLM exploration > traditional tools) generalizes outside domains with high uncertainty? Or is it specifically valuable where 'deciding what to do' is the hard part?
Someone else mentioned using Chrome dev tools + Cursor, I'm going to try that one out as a way to convince myself here. I want to make this work but I just feel like I'm missing something. The problem is clearly me, so I guess i need to put in some time here.
We'll see how many of these are around in a few years.
The agent loop architectural pattern (and that’s the relevant bit) is going to continue to matter. There will be new patterns for sure, but tool calling plus while loop (which is all an “agent” is) is powerful and highly general.
Right now models have roughly all of the written knowledge available to mankind, minus some obscure held out private archives and so on. They have excellent skills and general abilities to construct plausible sequences of actions to accomplish work, but we need to hold their hands to really get decent performance across a wide range of activities. Skills and agent frameworks and MCP carve out different domains of that problem, with successful solutions providing training data for future models that might be able to be either generalized, or they'll be able to create a vast mountain of synthetic data following successful patterns, and make the next generation of models incredibly useful for a huge number of tasks, by default.
It might also be possible that by studying the problem, identifying where mode collapses and issues with training prevent the right sort of generalization, they might tweak the architecture and be able to solve the deficiency through normal training runs, and thereby discard the need for all the bespoke artisanal agent specifications.
You can have the most capable human available to you, a supreme executive assistant. You still have to convey your intent and needs to them, your preferences, etc, with as high a degree of specificity as necessary.
And you need to provide them with access and mechanisms to do things on your behalf.
Agentic definitions are the former, and they will evolve and grow. I like the metaphor of deal terms in financial contracts- benchmarkers document billions of these now. The "deal terms" governing the work any given entity does for you will be rich and bespoke and specific, like any valuable relationship. Even if the agent is learning about you, your governance is still needed.
MCP is the latter. It is the protocol by which a thing does things for you. It will get extensions. Skill-like directives and instructions will get delivered over it.
Skills themselves are near term scaffold that will soon disappear.
Skill is a great sleight of hand for Anthropic to get people to think Claude Code is a platform. There is no there there. Orgs will figure this out.
Cheers.
However the "waiting out" strategy needs a timeout. It might happen that agentic crutches around LLMs will bear fruit much sooner than high-quality LLMs arrive. If you don't have a timeout or a decent exit criteria you may end up waiting indefinitely, or at least until reality of things becomes too painful to ignore.
The "ski rental problem" comes to mind here, but maybe there is another "wait it out" exit strategy?
I don't this makes any sense as MCP is a part of something they can do already
Sorry for the nit, but this is a gross oversimplification. Most private archives are not obscure but obfuscated and largely are way more valuable training data then the publicly available ones.
Want to know how the DOD may technically tracks your phone? Private.
Want to know how to make Coca Cola at scale? Private.
Want to know what the schematic is for a Google TPU? Private.
etc etc.
The reason I ask is that the pace of new things arriving is overwhelming, hence I was tempted to just ignore it. Not because things had signs of transience, but because I was drowning and didn't know where to start. That is not the same thing as actually observing signs of things being too foamy.
MCP lets you glue random assed parts of services to mega-ultra-high critical business initiatives with no go between. Delivered through a personalized chat interface that will tell you how sexy you are and how you deserved to win at golf yesterday… from salesman to auto interface to forever contract in minutes.
MS sells to insecurities of incompetent management and facilitates territory marking at the expense of governments and societies around the world for mega bucks. MCP, obvious as it is technically, also lets them plug a library into existing services for a quick upgrade then an atomized upsell directly to the chat interfaces of upper management.
Microsoft’s CEO has talked about his agent swarm. Much like RPA this woo appeals strongly to the barely technical.