I totally agree with this bottom-up style of software design. In Python, I start with dictionaries, tuples, and functions. And then later I might turn them into more structured classes and methods.
I'm not sure you need prototypes for this evolution, but I concede that it's plausible that they will help.
Actually I think Python is too impoverished in letting you make things stricter as the design evolves. I suspect the same may be true of prototypal languages. Yes they are good in the initial stages of program design, but perhaps the later stages are just as important.
A successful program spends more time being maintained than being written, and it's maintained by more people than it is authored by. So it makes sense to devote a good chunk of your language design to the later stages, and implement classes + metaclasses rather than just prototypes.
Anyway, thanks for the interesting perspective. Yes I concede classes can lead to early "over-modeling". But there's also a difference between Java classes and classes in languages like Python and Ruby. And classes vs. prototypes is not the only relevant issue when doing bottom-up, iterative design.