I've been reading comments on one of the articles I linked before, and I'm seeing some fairly common thoughts.
One is dealing with the size (understandable, as users really don't care all that much about the size of desktop computers), asking whether a unit merely 1/2 the size of the old Mac Pro (vs 1/8th) might have been better.
And the simple answer is that it wouldn't be. It would add expansion capability in some form, true. But your options are to go over, under, or next to the existing "core". None of those options work well. Going over means you're going to have some components getting a huge amount of heat thrown on them. Going under means you have accessibility (for repair/replacement) issues (and you're moving the most valuable parts into a less-stable position). And going "behind" means you break the thermal core, because it stops being symmetrical. Suddenly, some of that heat is escaping towards the side, instead of up.
I think the whole core is understanding that the heat sink drove the entire design, and that's why it's so forward-thinking, because heat requirements will have a hard time going down, while there are a few ways to improve the airflow with this basic design.
Plus, thunderbolt will cover just about any eventuality that you might need (assuming the graphics cards can be upgraded, which is, it's true, not a given).