"The bigger picture is that almost all hard R&D takes place under the umbrella of some sort of protection from copying."
There is a huge difference between protection from copying, and protection from building similar things that achieve the same goal. Patents are not simply "protection from copying".
Drug patents often cover things like "using the same body mechanism to achieve a desired result".
(Now, you can argue this is necessary to protect them, but let's be clear - it's not straight copying if i make a pill with a completely different chemical composition that ends up triggering the same mechanisms. However, it likely runs afoul of their carefully drafted patents.
I'm also aware there are chemical compound patents that would not cover me doing this, but usually, when the drug companies can, they get both)
"Intel spends billions a year on semiconductor R&D, and protects it with trade secrets"
and design mask protection (see https://en.wikipedia.org/wiki/Integrated_circuit_layout_desi...)
"Pharma companies spend billions on drug R&D and protect them with patents. "
They are also heavily subsidized, unlike your intel example. Tax payers, for example, pay about 50% of pharma's R&D costs (and pharma includes a lot more than actual R&D in R&D cost).
http://www.healthnewsreview.org/2012/02/the-costly-myths-abo...
and
http://www.thefiscaltimes.com/Columns/2012/02/16/What-Those-...
"Hard R&D that isn't protected from copying is usually subsidized. "
Pharma, one of your examples, is both heavily protected and heavily subsidized. Heck, Intel gets huge R&D tax breaks too.
In truth, most of the heavily protected stuff is subsidized by tax payers in various forms anyway.
The idea that these companies are out there, doing it on their own, without essentially getting most of the R&D cost subsidized through tax breaks/etc, is a huge myth.
We don't have the model you propose. We have a model where it is both heavily protected and heavily subsidized.