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.
Rob