Offering an automatic transmission without offering a manual gearbox would be a fairly good example of lean manufacturing - at it's core, lean manufacturing is "Less work, more value". The cost of developing any gearbox that would be used next year has already been invested. When I see automatic tranny as an option, it only adds value (base price and resale) to the vehicle. The consumer cost isn't higher because it lowers the vehicle value
A/C - I can kinda see that... Except home is S. Florida. I know of almost no one that would consider any vehicle without A/C. Regional? Absolutely. But if most of the vehicles you sell will have A/C installed - the ones without A/C are going to cost more to assemble (nothing happens to the vehicle while moving down the line - which is one of the most expensive processes you can do to any item on a production line).
The cost to tool a cup holder into a trim piece die (that needs to be made anyway) is insignificant compared to the apparent value it adds. After all, like the people actually buying new minivans tell us - 'more cup holders = safer vehicle.'
The issues you present are not so much that of lean manufacturing (I can go into more detail, I've seen some really great low volume applications locally). It sounds like you have a problem more with what's called 'custom mass production' or "Mass Customization." A very successful application that maximized this is the Scion vehicle line.
Volumes have been written on optimizing the number of customization parameters versus perceived value versus manufacturing costs. I personally have not read any, but am aware of their existence
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Of course, we must all accept... Well, most of us at least.... We are not a part of the solution. You bought used, not new. If you want a say, you'll need to do so by buying a new car that closest represents the feature set you want. If no one bought the Prius (or insight, etc.) - I highly doubt any other manufacturers would be developing hybrids and/or licensing the synergy drive train.
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Here's another easy way to lower costs..... De-automate. When designed for assembly, automation is incredibly expensive next to non automated processing.... The problem is, and it's a doozie, quality goes down the tubes. You'd lose high skill tech jobs (programming bots at about a $million each) but you'll gain low skill assembly work. I don't think this is the way to go - domestic brands are finally rebuilding their quality reputation (largely due to automation).
That said - automated optimized designs really piss off hackers and tinkerers.... Because one thing it means (generally) is no screws, no bolts. How many of you have come across a part on your car that snaps shut/together (rather than a screw or bolt?)
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If you're interested in Lean Manufacturing, I can recommend a book or two if you want (of course, they're kinda pricey).... Also, you might want to read about heijunka and production leveling (basically, what good is a 500 part per day machine if that stock waits in a warehouse for 3 days before use?).
Plenty cost savings can be had by applying heijunka techniques. I see no reason why the dealership system needs so much stock on hand to later become a tax burden.
But, Lean manufacturing, production leveling, etc. etc. does not address the issue that 61 vehicles rather than 400 were sold
I'm willing to bet it wasn't Ford's choice of using a specific brand of spot welder robot that made the customer move to another brand