Besides real problems regarding binary formats, its psychologically most destructive property is that everybody has the self-proclaimed best encoding, the fastest encoding, the most space-efficient encoding, the most flexible encoding and so and so which only differ in one of two bits somewhere and therefore makes them 100% incompatible. Thank you.
Why? Because binary is the way to go if you want fast, efficient, direct, buzzword, buzzword, ....
Look at text-based format. Do all these requirements matter there? No. Their implementors focused primarily on the content in conjunction of readability, maintainability, flexibility, expandability and independence. All properties, which are required for the maintenance of long-term applications.
+1
Besides, in my experience good compression will almost always beat any attempts at "clever" bit manipulation and is mostly transparent.
This paper looks like a typical case of a computer scientist with not much real world experience trying to teach programmers how to do things...
From my experience, a well constructed binary protocol can provide tremendous advantage when used properly. Also from experience, I would recommend using a Type-Length-Value (TLV) messaging structure to facilitate expandability and maintenance. Endianness is easily dealt with. Additionally, the binary bytestream may benefit further with addition of compression algorithms, assuming the data is non-random.
The P2P transport mechanism is THE core component of the platform, and should be optimized. Parsers can be built to translate into more usable structures.
My 2 NXT, FWIW.