I really don't have too many gripes myself, though you did touch on some things that I've dealt with, a bit grundgingly. Per your list:
#1 In And Outs: I personally don't have any real issues with the jackfield being on the top, and if anything actually prefer it as it allows for slightly tighter horizontal pedalboard layout, and works nicely with some of my other pedals using the same jacks-to-the-top configuration (i.e. Strymon Lex, TC Nova Delay, Digitech Stereo JamMan).
That said, I definitely do also find the input/out positioning on the top annoying with the inputs to the left and the outputs to the right, as this is reverse of pretty much every other pedal I own, both with jacks-to-the-top and jacks-on-the-sides: flowing from right to left. Running stereo here as well, so am also dealing with the criss-crossing.
#2 Midi Ports: agree that their position on the side can get in the way and eats up precious horizontal space between pedals. But on the other hand: I can also understand that had Eventide mounted it on the top with the other jacks, it would've likely required an increase to the pedal's width to allow for the jack diameter itself (and negating any horizontal space advantage gained by moving the MIDI jack to the top) , or an increase to the pedal's height.
I'm using a right-angle MIDI cable between my Space and PF, but it being that the cable's plugs are revered on each end, I have to make one of the two pedals raise up on a small pair of wooden blocks to allow the right-angle connection on one of the two pedals to go downward (my main pedalboard isn't an open design like a PedalTrain that could possibly allow for that). Annoying, but something I can deal with.
If I had a wishlist item in regards to the MIDI jacks, it would've been that they been rotated 45 degrees to allow the right-angle plugs to aim towards either the bottom or top of the pedal, instead of downwards or "pointing up like fountains at the Bellagio" (good description, fjurden! 
)
#4 Power: I guess I seem to be one of the minority out there who doesn't have any real issues with using the wall-warts a pedal might come with (heck, I actually appreciate it being provided at all! ), so I have no problems with using the two that Eventide supplies with my Space and PF. To free up space on power-strip, I just use those cheap "mini-extension-cords" that are maybe 6" in length, so the wall-warts aren't blocking up space on the power-strip itself but lays next to it. Yeah, it's butt-ugly…but that doesn't really bug me personally, and I tend to play in darkened studios or stages anyway… 
