One ‘whatever’ where it doesn’t win is in robustness. Code will make assumptions about various kinds of animal and fail when meeting a sheep with 5 legs, or a pig that can fly.
You can solve that by testing for capabilities, but you would have to do that in many places, and make sure to cover all of them.
And yes, that comes at the cost of flexibility. Your class model won’t support flying pigs until you consciously add such support.
The other thing I suppose is multi developer environments - classes and compilation win out over prototyping because they're easier to split up. There might be other reasons, but that's why I always come back to class based programming, the idea of prototypes is very enticing though.
Edit: though I have started to use a pseudo prototyping environment - breakpoints and evaluate when things get complex, though its not the same.
What is so bad about that?
And isn't it common practice around computer games for example, which can be modded and extended by custom user content?
But now, switching between a terminal that uses shift-ctrl-c for copy, and outlook/o365 in chrome, I often accidentally open developer tools in my email "application"... And wonder how much better we might be off with a solid smalltalk (or strongtalk, self) system -- than the current mix of crappy web apps and crappy electron behemoths...
I should note that it's generally possible to strip out/hide and disable most of the introspection stuff from smalltalk applications and ship more end-user style applications.
Sure, programmable by what today we'd call "programmers" but certainly not by "users." This is because programming has become a niche trade (as I said before, like a scribal culture).
I'll give an example. Most users' experience with their host Operating System involves prodigious use of buttons. They know how buttons work and they know how to interact with them. But in all these OSes it is extremely difficult for a user to make a button that does something they want, then, say, place it on their desktop for future use.
In the past there were really good attempts at authorship in computing media (which is more like what the LRG was going for with Smalltalk etc), including Hypercard. In the latter system, you could pop open a button and see how it worked in a comprehensible scripting language. You could copy the button and paste it somewhere else. You cannot do any of this with buttons in the major OSes. The capability is not there.*
The only option available to "users" is to learn a full fledged, general purpose programming language with all the pitfalls that entails, which means learning build systems and all the rest. At that point they have to become what today we call a "programmer," ie a scribal-programmer.
Our dominant systems have been explicitly designed for a strict delineation between scribal-programmers and consumer-users. That's the rub.
* - AppleScript is a so-so attempt at this, but even that has been allowed to die on the vine.
I'm not against them - these are reasons I can see for not using prototype languages.
Edit: I suppose to the environment a developer wants isn't the environment that a game user wants, like a game user wants to just extend a few things - but having the whole self environment for arguments sake would be fairly intimidating I'd imagine.
With FP you can simulate both class based approaches and prototype based approaches. The slightly 'warped' perspective of the FP lens might give you more insights into your question.
(I can expand, if you are interested.)