Being able to select/designate individual pins as 5v or 3.3v logic
Needs a lot of hardware, in banks of 4, 6, or 8 not so bad.
A crosspoint switch would be one way to go, you'd need a lot for them and last I looked they were not cheap. Also I don't think they level shift but at least they should pass the analog.
As for the analog you can get programmable gain chips or just make your own with opamps.
Either way you need more IO to control this lot, so add 1 or 2 I2C IO expander chips with jumpers to set the address so they don't clash with any shields.
In general I like the basic concept but it could very quickly turn into a cluster f*ck with 30 chips that cost 2x the Due and the shield you want to use.
Crossroads (aka derekmjenkins!?), you've obviously made a start, any thoughts on doing something?
Are there many mega shields?
I don't think so, I'd drop the extra stuff and just go for a standard shield.
EDIT: I just looked at the price for that CD22M3494 crosspoint switch, it's not too bad but still too much for this I think.
Hey Rob, got a solution for ya. http://www.ti.com/product/sn74lvc16t245
(I think there is a 32 channel unit as well)
Use something like this after a crosspoint switch and before exiting the shield. That way, each pin's output voltage can be selected and each pin can by dynamically assigned. Also, why do you think this would be too expensive? Mouser has the level shifter I just mentioned at $2 and the crosspoint at $4 or 6. Plus other parts and custom fab, you could almost surely get away under $20.
EDIT: Just thinking, you would just need the crosspoint for the pins that need to be moved like SCL and SDA, then just use a couple more of the level shifters I mentioned for the rest of the I/O. That way, the pins that might need to be moved can be, while all the pins can still be selected to be either 5v or 3.3v.