The last upgradable mac is now dead. I thought the whole idea of the pro was the ability to put in graphic and other specialty cards as needed for "Pro" use. This looks like another cute consumer PC. Maybe they'll sell it along side the HP's at Sam's Club.
I think the idea here is that, between plentiful Firewire 2 and Thunderbolt 2, you now have enough external bandwidth that you shouldn't need internal cards. When given the choice, I prefer this route, since it means I can transport my proprietary stuff to other machines, or even use them with laptops in a pinch.
That might not work for you, granted, but the amount of bandwidth available between all those ports (20 GB/s in the case of Thunderbolt 2) should be enough to cover most use-cases.
I would have designed it the same way - Thunderbolt is the future of expansions, not tiny little cards you need to slide inside of the HW. This machine recognizes that - They give you 6 (six!) to play with.
Thunderbolt IS PCIe, so it's just as fast.. Why should card makers be constrained in expanding the machine to make peripherals small enough to fit inside? If I want 1 solid foot of Disks for my workstation, then so be it. Wire it in over Thunderbolt, and I'm good to go.