What about FPGAs? I feel like they could solve so much of this problem if the tools were better. Though I haven't used them since college, so I have no idea what the current status is.
Hell, FPGAs are Jedi-Master class devices as far as I see it. This is the kind of firepower you call in when you have something that no off-the-shelf micro can do, like emulate an obsolete processor, or put 128 of them on one chip, or hash Bitcoins, image processing, etc etc etc.
For example, it would be cool if there was some sort of software that would let you design multiple-chip setups that would usually require breadboarding, but then run the whole circuit on the FPGA. That design could be transformed straight into a PCB that's ready for fab with the discrete components.
I actually see a lot of potential in devices like the aforementioned Cypress PSoC. If you're not familiar, the PSoC family involves chips that have a core microcontroller with ram and Flash but also have a number of analog blocks inside as well. ADCs, capsense, op-amps, logic gates, muxes, comparators, timers, etc. You can use the Cypress IDE to wire the components up and connect them to I/O pins. The IDE can generate your configuration, or you can optionally reconfigure the chip while running via internal registers.
So it's kind of like an FPGA-type solution as you suggested. When you start developing with these chips, you're really creating hardware from software. It's interesting stuff.