Personally, I am torn as I am often known when I build a breakout board to end up cramming as much stuff as I can possibly add as I maybe I will need it some day, which sometimes makes the boards a pain to build...
so my 2 cents worth:
So personally from maybe a page back, I always want as many uarts as I can get. I personally don't use too much I2C, but do a few experiments with them (lidar lite). SPI - two would be great, with maybe one dedicated to things like SD cards and the other to things like display... I am a junky for IO pins, but honestly there are very few times I have come close to running out of them on the 3.1...
On form factor: I personally liked your idea earlier on, which was thinking of the products like a family of products. With LC at bottom end, new one at high end and 3.1 in the middle. Where maybe one could design a board that you could plug in any of these, where the 3.1++ would simply extend another inch or so... Sort of like Arduino vs Mega...
But if you deviate from this with different connectors or pin spacing, I hope you still take the hobbyist into an account.
That is for example with Edison, I personally am not great with soldering really small pin spacing like the hirose (sp) connectors, so I would have to rely on someone else to make a breakout board. So now I have two boards to buy. Also you just added the extra expense of these connectors. Note: I am not putting down the Edison. There are parts of them I like, but their support of them can be a bit frustrating...
Personally I am not against somewhat smaller pin spacing. Example I have built XBees into some boards with the 2mm, but they can make it harder to design boards as typically I don't like my etches and spacing's to be that tight, so typically can not run etch between pins.
As for other boards that use different pin spacings? Currently I am using a couple of the Odroid XU3-lites (maybe soon will try newer XU4
http://ameridroid.com/products/odroid-xu4). They use I believe 2mm connectors (with 1.8v logic). So to experiment with their signals, I needed to purchase some jumper cables (adafruit) that had the 2mm female to 2.54... to jumper to breadboard to try things out (through level shifters...). They also understand that issue, so they recently released a level shifter board (
http://ameridroid.com/products/xu4-shifter-shield) that both allows the user to choose 3.3v or 5v, plus brought out the signals out to a .1" spacing connector that is compatible with RPI (as well as their Odroid C1). As to allow some of the RPI shields (like display) to plug in...
So again personally I think you should at least for the exterior pins keep to the .1" spacing hopefully as compatible as possible with 3.1. As for the interior pins, by definition these don't plug into breadboard, so could be different spacing. However if you choose a different spacing hopefully it wont be too small (2mm?).
But again that is just my 2 cents.