Rezzes being allowed in duties that previously didn't allow for them is really just bringing those duties in line with the current design strategy of content that uses similar knock off mechanics.
Coincounter was fun when the max level was lower. Now it's very solidly in the entry level portion of content so I don't see it as an issue, especially considering how the first room still sucks to this day.
The lack of exploratory zone is something I would personally call a good thing. Bozja and Eureka were not future proofed and can be difficult/impossible to progress in depending on your world/DC.

For anybody who thinks I'm making excuses for mistakes on SE's part; I'm not. I don't consider most of OP's points to be mistakes in the first place.