I'm in the industry and this is almost certainly software related. Simplistically there are two types computing systems, PCs/Laptops/Servers/Consumer electronics, and then embedded systems, things like cars.
Embedded systems often need to respond quickly to unexpected inputs. I suspect Microsoft sucks at writing an operating system that handles that well and if Sony had any hand at writing the SW that could be an issue too.
Also, the car companies have historically bought the car stereo and nav systems from third parties. There is a move to where the car companies are buying hardware from one supplier and then they are writing the SW themselves. I suspect that Ford and Microsoft wrote it and they have lots of bugs and mistakes. Could even be the fundamental SW arch.
I will ask around a bit to see what I can learn.
MFT runs on top of what is more or less Windows CE. If you ever had a windows CE or windows mobile smartphone (NOT windows phone, that's newer, totally different) you know how bad this OS is in terms of responsiveness and just overall bugginess.
I'm a software engineer myself, I've actually written a very similar system on top of Windows for the trucking industry (if you are familiar with qualcom, peoplenet, etc you have a rough idea what I'm talking about). Building the system on windows was NOT my call though, I would have chosen to go with linux. Windows mobile or "windows automotive" was probably dictated to the ford engineers the same way it was dictated to me "we've partnered with MS, now go make it work"
Systems like this have to follow a fine line. "Responding quickly to unexpected inputs" as you say, is best done by a real time OS, however those are historically much harder to code for, and much hard to update, and generally much "closer to the metal". They also aren't really necassary unless you need response time in ms, which is usually only needed for embedded control systems etc. The ECM of the truck is a good example of a real time embedded system.
On the other end of the spectrum is the traditional desktop os (desktop windows, linux, osx etc) which have task schedulers etc and respond to hardware inputs "when they get to it". The advantage though is that you can easily code up background processes etc, you have access to "higher level" languages and libraries (think building things with legos vs carving it out of stone).
The trick with a system like this is to strike that balance between real time and easy to code for, update etc. It would have helped if they'd started with a solid foundation with slick/fast UI libs etc, but that is most def NOT winmo.
Also hardware always helps, IMO the MFT system is very underpowered in terms of cpu/ram. The freescale cpu was top of the line in 2005 maybe, in 2013 it's a joke. It's obviously about cost, Ford pays < $30 for the MFT board. The cheapest android, windows phone, or ios device you can buy will run circles around this POS.
IMO the best example of how to do this type of system "right" is the Tesla model S. Android (linux) based with ample (nvidia tegra)hardware, and it is SLICK. Then again it's also a decade or so newer (wince/"autopc" came out in the late 90's and at it's core that is where it remains).