I think you must have missed the big discussion when the changes were announced.
There was also a really handy wowhead article explaining how to get about after the changes.
They have read the feedback and in the latest Q&A stated they will be adding in a portal to CoT as that seems to cause the most issues.
What will be done to address the removed portals?
They don’t want to rehash the reasons which they already posted on the forums. There are valid reasons. With every expansion they’ve removed some portals.
They’ll be adding a Caverns of Time portal that takes you directly into the central Nexus. There’s also another UI update coming soon which will help you travel to another continent when an quest is tracked on another continent.
I think most players have covered your specific issues.