I do think the show's doing some hindsight history with MacMillan's health. My understanding is that in 1963 medicine, he doesn't quite have the clean bill of health. I haven't seen this interpretation, but I thought the Queen's speech to MacMillan was a Be Careful What You Wish For foreshadowing, with her emphasis on "men" and "staying the course." One thing that added to the controversy, which was under-discussed were the rumors that Margaret was sleeping with Douglas-Home's nephew.
The problem with Philip IMO is as much storytelling as the character. They keep repeating the same plotlines. Also, I think there's a genuine affection the writers have for QEII so in every dispute he has to come across looking like a heel. For instance, everyone says that Philip is the most powerful consort ever, which is wildly untrue. When people say that he knew what he was getting into, he may have thought he was getting the same role as Prince Albert.