You make some valid points and I can say that I share some of those concerns but only to a point.
The 7.3 and 6.0 diesels are loud, clangity, bangity, rattlin' SOBs. I can only think of two stock engines louder and more obnoxious than either of those. One would be the 6.9 Ford and the other is an old CAT engine nicknamed "The Buzzin' Dozen". 12 cylinders of eardrum busting, bowel shaking diesel wonder.
Technology has changed a bit...the new 6.7Ls are super smooth and quiet. I think it will still be what it is...a van with an engine half inside the cab...but the noise level increase of the 6.7L over the 5.4L isn't keeping me up at night with worry. I don't think it will be much different at all, especially after I redo my interior. I can't even hear my engine half the time now because the junky, cheapo interior panels squeak so damn much!
The weight is definitely going to change things but it can be dealt with. I plan on doing some suspension upgrades as soon as I know what the weight distribution is going to be.
One of my previous jobs involved a lot of interaction with stress testing engineers at the big three. The biggest driver of a lot of the testing we did was cost reduction. Or better put, how little money can we put into this part (or assembly) and how little effort can we expend in manufacturing and still have it perform to xxxxx level. Cars aren't designed to be great, they're designed to be good enough and cheap as possible. The E-series is definitely not getting the engineering love that something like the Mustang gets. You can tell they just throw them together and put as little effort into them as possible. There are parts on my new van that interchange with a '92 for crying out loud. If anything, I think that all the effort I'm putting into my van is making it better and more reliable.
I'm sure things will come up and have to be dealt with. It's all part of the process.