I think you're overstating things. Generating x86 output from an intermediate language really isn't that bad. Is it what you would come up with if you were designing an ISA from scratch, but it's hardly rocket science either.
More to the point: the real determining factor for "CPU uberness" isn't the ISA at all, it's the process technologies. Modern x86 CPUs aren't exactly handicapped; in fact they're pretty much the best parts you can buy in almost all major market areas. Other architectures at this point are increasingly niche parts: very low power (the ARM family, although Intel is moving into this market as we speak), or very high parallelism (Sun's Niagra, IBM's Cell), etc... If any of the stuff you're complaining about really mattered, it ought to be a competitive advantage to someone, no? But it's verifiably not.
I fully agree, but I was asked for why I don't like the x86 architecture, so I gave an answer.
Current x86 CPUs are pretty awesome when it comes down to it. the ISA is quite hairy, and that makes writing tools for them quite a bit more painful than for, eg, mips, but because compilers are good you don't feel the pain from using x86 anymore, so nobody cares -- or should care -- that they're actually using x86.
More to the point: the real determining factor for "CPU uberness" isn't the ISA at all, it's the process technologies. Modern x86 CPUs aren't exactly handicapped; in fact they're pretty much the best parts you can buy in almost all major market areas. Other architectures at this point are increasingly niche parts: very low power (the ARM family, although Intel is moving into this market as we speak), or very high parallelism (Sun's Niagra, IBM's Cell), etc... If any of the stuff you're complaining about really mattered, it ought to be a competitive advantage to someone, no? But it's verifiably not.