I can appreciate that it's late in the design cycle to make any request for connectors but has the Parallella team considered using a standard connector like FMC.
I think that the current connector selection is great for high throughput but it offers no path for quick prototyping that simple .1 inch headers have. I understand that .1 inch headers leave something to be desired in the realm of signal integrity but that's where FMC boards come in.
What's great about this standard is that you leverage the pre-existing daughter cards that are out there. If people want to buy a board with .1 inch headers and play around with their board then they are free to do so. Future Parallela boards can use the same connector as well as taking advantage of all the gigabit transceivers that you can get when your team may switch to a higher end Zynq chip.
In my opinion you will loose some of your market due to the pain associated with building a daughter card with a non-standard connector. I hope you can hand solder that connector because if you can't that means that every daughter board is a significant investment.
I'm not trying to troll here but I think TI has learned their lesson with the BeagleBoard. It came with two row .1 inch header with a 1.8V level which was a pain in and of itself because the first thing you had to do was level convert that signal and the highest throughput bidirectional communication was a spi bus. I was going to build a daughter card but even that deterred me. After a while they came out with the BeagleBone and now you can play around with an idea by wire jamming and a bread board instead of making a significant investment into fabing your own PCB.
I've built 4 revisions of an FPGA development board and more times than not I'm working on it at my desk. So if it's a little larger but easier to use I will be much happier.
Dave