Ive pondered this question for a long time. More and more new cars have larger and custom shaped head units, built in with info panels/screens and combined with temperature knobs etc....sure it looks better for the majority of the people who are not interested in aftermarket car audio but what about the rest of us who dont want to settle for the stock equipment? What can you do without completely ruining the aesthetics of a new car?
I would like to mention that although I enjoy aftermarket car audio systems, I am not into any other customization on the interior of the car,
It's becoming more of an issue with nav/touch screen head units, as well as those with integrated climate controls, definitely. I've thought about this as well.
As a result, adapters to fit in aftermarket head units are becoming more pricey (especially since the adapters have to bypass computer systems etc. now).
Usually, though, you can still upgrade the rest of the components, such as speakers and external amplifiers. And really, adding a set of components and sub with an aftermarket amp or two will make most factory sound systems quite a bit better. On the bright side, factory systems are becoming better and better anyway, with front tweeters and CD players stock, as well as bigger front speakers. A center channel surround speaker seems to also be increasingly common on more premium models (however, surround systems in the aftermarket world are still in their infancy, in my opinion). Factory subwoofers are also becoming more common. Finally, we're also seeing car audio companies collaborate with car manufacturers to create sound systems: Alpine (Mercedes-Benz, BMW, Acura, Volvo, Aston Martin, Jaguar and Land Rover),Blaupunkt (Audi, Volkswagen, Porsche, Mercedes, Vauxhall and BMW), Bose (GM usually, Nissan, Cadillac, and others), Pioneer (some Toyota models), Clarion (Honda, Hyundai), Boston Acoustics (Chevy), Dynaudio (Volvo), Audyssey (Jaguar, Volvo), Harman Kardon/JBL/Infinity(Mercedes-Benz, Toyota/Lexus, BMW, GM), Bang and Olufsen (Audi) etc. (the list goes on). So it's not so bleak.
As long as the stock head unit is big enough, though, and as long as climate controls aren't built in, there will always be a way to integrate head units (rather easily, I might add). Though like you mentioned, it would be hard to make an aftermarket head unit look good in some of the consoles in some of the new cars, or even find a place to fit it. One example are new Volvos, especially those with the floating console. A new head unit would have to be VERY custom, and they are using optic cable for all of the components in the higher end systems, so the entire system either has to be replaced, or bypassed in a very complex way.