In US copyright system there is the notion of mechanical royalties where I can use any songwriter's work without a negotiated license. I record my usage, and there is a rate (cents/minute). Now, I am free to negotiate a different rate with the songwriter if so desired, but there is a compulsory aspect where permission from the original author is not required.
How about applying this to the patent system? Like in the copyright system, a collection of patent judges could determine the relative worth of a patent, examining not just the patent itself, but various aspects surrounding it, such as barrier to entry for the market, (non) obviousness, complexity, and usage. A patent on a large-scale industrial manufacturing process would cost much more than a simplistic patent on a method of how to use child's swing. The patent can then be licensed by anybody on a per-unit basis for this rate, but alternate rates can be negotiated, possibly in a lump-sum instead of a per-unit basis.
The largest effect this would have is turn patents from a (per-claim) all-or-nothing game, into a game of degree. It is already up to patent examiners to look at the sheer validity of patents, giving them an additional level of control does not sound infeasible to me. This also wouldn't be cost-prohibitive like requiring a function prototype.