You could make a standardized GPU instruction set but why would anyone use it? We don't currently access GPUs at that level, like we do with the CPU.

It's technically possible but the economics isn't there (was my point). The cost of making a new GPU generally includes writing drivers and shader compilers anyway, so there's not much of a motivation to bother complying with a standard. It would be different if we did expose them at a lower level (i.e. if CPU were programmed with a jitted bytecode then we wouldn't see as much focus on ISA as long as the higher level semantics were preserved)