The largest issue with the trashcan MacPro6,1 was complete lack of GPU performance. They weren’t even VR capable.
The biggest problem is the form-over-function design. The same applies to the new one as well, though it's not as bad. In both cases, they are missing out on the business market who need a workhorse. Both are priced out of most people's budgets. We end up buying Mac Minis and struggling with their limited capabilities and expansion options. Their whole strategy here is poor. They don't have any midrange options between the two extremes.
For a while, the software quality of new OS releases was night and day, comparing iOS and OS X. It was clear where the focus was. Apple's org structure has it's weaknesses.