Outside of 64-bit mode you can't do byte operations on [e]si, [e]di, [e]bp or [e]sp (though for the last of those, there is little reason you would want to). In 64-bit mode, you can do that with a REX prefix, but then you can't access the ah, bh, ch and dh. There's only one size bit in the main opcode byte so they had to add a prefix byte when they added 32-bit support and another one when they extended to 64-bit. Unsigned multiply instructions have a fixed destination register/register pair. Numerous instructions have special shorter encodings you can use for certain registers.

All of this makes a lot of sense in the context of the 8086. It needed to be easy to port assembly from the 8080 and memory was incredibly limited. As a product of its time it seems like a pretty good design, but it wasn't a forward thinking design. The 68000 by contrast was a (mostly) 16-bit implementation of a 32-bit, forward-looking, ISA. It's a shame x86 survived while 68K is mostly dead.