Yep guess we should be thankful they have one add-on board I suppose.
Also, yes, there is possibly the case of "we can sell them an adaptor for that too" type approach. I guess it makes it more lego like, which is a good thing I suppose.
It is just the fact that I2C was so carefully designed to only need a few wires/connections, goes against the grain a little to make use 20+ extra.
Mind you, I guess if there was a standard-ish I2C connection, then they could keep the full header and easily add a few pins to allow daisy chaining of I2C devices (and an alternative way to connect) - the obvious advantage to them is selling multiple devices. If using the 2x3 header option, it wouldn't even matter if you had full 2x13 connection or not (as long as there is clearance).
Using the unit with breadboard/stripboard would be difficult, but I guess using M-F jumper wires would be possible. Also you could mount 2x3 connectors on a stripboard (with careful track cutting), as it is only a few pins to carefully solder in place (can keep the fall-back option of the 6x1 header anyway).
2x3 Connector which matches top pins of P1.
Colours (if available):
Only confusing thing might be that the pin one wire will be orange.
We would still need a converter for P5, which while you were at it would need to include 1K8 pull-ups on anyway, so it would help to have a different connection here. Oh, and the added fly...have to consider top/bottom connections...which is helpful!
I think at a push a 1x6 variant can be used, for cases where it is easier design-wise.
Missing for polarization
I don't know if we would want to include a blocked hole/key in the cable for the missing pin (making it a problem if there is a pin there, like on the RPi itself or on a full header), or let it be inferred by missing pins on the devices by not having a wire going into it. My preference is the latter of the two. It could be optional to use a keyed connector as it should still work with open pins (as long as it doesn't get in the way of other pins on a full header).
I think in general the proposal has more advantages than disadvantages over picking some other arbitrary arrangement. The simple 1 to 1 wiring for beginners would be very helpful.