Having maintained Deadly Boss Mods for nearly twenty years, Mystical has a wealth of experience in unraveling the intricacies of WoW development.
First and foremost are the many bugs with boss warnings, duplicated or overlapping spell IDs, and event timelines. While bugs in a game this size are nothing new and even expected to some degree, what Blizzard's addon restrictions have done is make it much more difficult for addon authors to address them.
Over queuing timers that players don't need to see is one of many common bugs.
That goes hand in hand with what Mystical refers to as the lack of user agency; the inability for players to customize the feature to suit their needs. DPS are still sent timers for tank mechanics, and Blizzard decides what needs to be emphasized whether you explicitly need a warning or not. Ironically, Blizzard's feature supports three levels of warnings based on the severity of mechanics, but very rarely ever use more than one of them... resulting in every alert being treated with the same priority.
There are three levels of warnings, though encounters seldom use more than one.
Perhaps the biggest takeaway is that while these changes are intended to even the playing field between players, that gap is growing even wider, particularly as some players may be mislead into thinking that Boss Mods don't do anything more than the native timeline. Though the API changes were meant to regulate addons to merely cosmetic customization for the built-in features, Boss Mods once again offer distinct improvements, though they need to use increasingly convoluted workarounds to untangle the mess left behind.
While curtailed, some mechanics still use addons to solve them.
Offsetting the criticism, one success Blizzard did make with these changes was curtailing computational problem solving. With the exception of L'ura, there is very little in the way of addons automatically directing players to solve encounter mechanics, though the Midnight Falls encounter is really just another example of the arms race between players and developers. For all their talk of affording players the time to recognize, react to, and solve problems, this particular encounter still requires 15+ players to coordinate split second reactions in a way that's just not feasible without addons and macros. Perhaps Termination Matrix don't need to orbit the boss so that players can more easily distinguish which they're meant to interrupt, or the four casts that need to be interrupted could have different names so players can more easily identify which they need to kick... whatever the case, we can consider it an exception for now.

