Though I speak from a probably utterly uninformed + unqualified standpoint, this raises a few points for me:-

1. If x86 hardware is so terrible (and I have heard that the architecture really is bad many times), how come we don't have competing chips out there which are many, many times more efficient? I know ARM outperforms on the low-power front, but not in terms of perf to my knowledge. Do such chips exist? And if not, why not if this is true? Even with x86 backwards compatibility concerns, you could bring out a theoretical amazingly powerful chip and just port compilers to it to leverage it and gain some (possibly niche) market hold that way.

2. I think he is underestimating the vast complexity of computing, and deeply underplaying the techniques which have evolved to get us where we are. Yes, I have again heard that the Von Neumann architecture has shortcomings, but look at what computing has enabled us to do - it has changed the world + enabled amazing things which are evolving at breakneck speed. Again - if there really is an ideal alternative approach, why isn't it being pursued? I don't buy the conspiracy theory crap about vested interests holding it back. Again, you could do well in a niche if the alternatives really are that much better.

3. I think it is likely that as things evolve previous ideas/approaches will be overturned and old approaches thrown away, like any pursuit. As @deweller says, this is true of any field. Ask any professional and they will tell you how their industry is fucked in 100 different ways. It is frustrating to hear software engineers talk about how terrible immature + hackerish + crap it all is while assuming that things have some sort of crystalline beauty in other industries. I did Civil Engineering at (a good) university, and it turns out that most consultancies use linear models to model everything, then apply an arbitrary safety factor, resulting in hopelessly inefficient over-engineered structures all over the place + turning the job into something of an uncreative administrative role in some respects (with no disrespect intended for all the civil engineers out there).

4. It is my theory that any attempt to interface with the real world and actually do useful real things results in an enormous amount of uncertainty and chaos in which you still have to make decisions however imperfect and however negatively others will judge it going forward. I think that's true because the world is chaotic and complicated and imperfect, and to influence it means to be touched by that too. That doesn't excuse poor engineering or not caring or stupid decisions, etc. but it is a factor everywhere I think.

5. So change it :-) there are efforts afoot everywhere to struggle to improve things, and from the sounds of it the guy has perhaps not tried enough things. I feel go is a great step in the right direction for a systems language which removes a lot of the crap you don't want to think about, as does C# (though it does potentially tie you to ms crap).

6. Programming is difficult, solving real problems is difficult, abstractions are nice but leak, and sometimes it's quite painful to have to put up with all the crap other people hacked together to make things work. But the value is in the end product - I don't care that my beautiful macbook air runs on a faulted architecture and some perhaps imperfect software, the beautiful ease of use is what matters to me. We mustn't lose sight of these things, though again this is not an excuse for crap code. There is definitely a balance to be struck.

7. Zack Morris is clearly a highly accomplished + competent hacker given what he's done and the obvious passion he writes with (to care enough to be disappointed + upset by these things is indicative), which I think has a bearing - the deeper your knowledge, the better your skill, the more faults you notice by dint of your intelligence + competence. There is a definite curse at play here.

Anyway, just my 2p :)