Probably too late to provide inputs but I got my Parallella a week ago and I missed a JTAG connector.
I mean I discovered the Zynq a couple of months ago and ordered the Avnet MicroZed board. I must say it was instant love with the Zynq!
Then I found the Parallella which is much cheaper and it's got the Epiphany chip on top. Frankly speaking, right now I'm not into Epiphany but this is something I'll definitely take a closer look at later on.
I understand that Parallella's focus is parallel computing but I guess there are folks out there who are looking for a cheaper alternative to the MicroZed and the ZedBoard and I think a dedicated JTAG connector on the Parallella would be a big plus.
Then something like PMOD connector/reset button/boot mode jumper would certainly be nice... just my 2 cts.