You do realize that it's illogical to compare about two spells side by side with no other kit interactions, effectively demand that one spell matches the other without considering other differences in the spell and/or kit interactions, then start a counter argument around considering whole kits, yes?
A lot of posters were proclaiming that WHM would've been dead on arrival and that was the crux I was aiming for. In reflection now, we know that would've not been the case. Just to reiterate some of what you've said, Thin Air is amazing, the changes to Divine Benison makes it much more usable over Stoneskin, and the change from Shroud of Saints to Lucid Dreaming offer WHM much MP sustainability and removed WHMs one of two largest flaws - MP consumption. The other flaw I see is a lack of raid utility but to be fair, I'm honestly okay with this given high DPS and nigh infinite MP. S-E certainly missed the mark with both PI and Lilies on its inception but by removing the one critical weakness to WHM sustainability, they've pushed WHM to be a very competitive healer as a no frills healing bombshell.
My complaint towards that initial mess of 4.0-pre-release is people being non-constructive with their comments and spreading misinformation. I keenly remember a few posters doing ability counts and proclaiming that WHM kit continues to be pruned and pruned and pruned without having replacements. Yet when you get down to the nitty gritty and look at each kit logically, WHM did indeed have less abilities but not 10+ less abilities that some posters were proclaiming. It's information like this that doesn't give the developers good insight on how to constructively change things.
With the above being said, I do feel it's important to be continue to be critical of changes but at the same time don't start to second guess what could be happening until you get to see all the changes in their entirety. It's difficult to give a thoughtful and constructive response until we see the entirety of the changes. I am also be cautious about changes from the development team in the healing department due to these missteps that you documented in your post. However, I feel someone claiming that we're moving towards the healer imbalance that was shown in 3.4 does feel a bit extreme and premature at this juncture without more information.