When 90% or more of the new car buyers do not care in the least whether their car stereo is flat to 15,000 Hz, or that the bass and sub-bass are truly linear with volume changes, do you think that they're going to spend and extra $100 per car to put in top quality speakers? Not when you consider that that $100 times 50,000 cars amounts to millions of dollars in lost profits.

I think that right now we are living in the golden age of car audio. Enjoy it while it lasts.

I think that's a bit pessimistic. Sure, the local installers may have issues, but I think the overall market is bigger now than ever before, and the supply chain has changed dramatically over the last ten years. It is no longer necessary to buy only the amps or speakers that are within a reasonable drive from you - the internet has changed that significantly. Ok, so mail order was possible before, but web transactions are so much easier. Ebay has exploded the second hand market, and information about brands and models (and how well they work in you car) is easier to obtain. Granted, you have to learn how to filter out the noise but...
There is a big issue with integration of the HU with newer cars. But ultimately the big OEMs will work around that one. Standards for integration with other car systems will evolve, and life will go on. Sure the paradigm is shifting, and companies will need to change. I fully expect that includes car companies. Already, the stock or factory systems in many cars is far superior to those of a few years back. But you are right when you say they will have financial limitations on their quality. However we will eventually see competition. At the moment we are seeing strategic partnerships, which are part of the transitional stage. When potential Lexus customers decide that they'd rather own an MP3 capable car stereo than one with the Mark Levison brand name, Lexus will start to consider an open architecture again. When VW start losing sales to Ford purely because the Phatbox is crap, and the Visteon rocks, they will start thinking the same way.
I don't think that the car manufacturers have lost the plot on this issue. I do think that they're having a difficult time coming to grips with the whole integration thing, but they'll get over it.