Personally, instead of EXes, I think that it would have been a better idea to shorten the game to 40 cards/4 prizes and design the game with that in mind. I tested out a format like this (that also eliminated basics over 90 hp and a number of trainers I felt were ill-advised) towards the end of generation five, and while it would take a lot of testing to maintain something truly balanced, I think the underlying philosophy was far more sound than what we got.
Also, while there were some precursors in early BW sets, it seems like there was a fundamental shift in species emphasis once EXes hit, to the great detriment of many BW Pokemon (which I liked-yes, even the ice cream cone).
I do wonder if the current dynamic is a misinterpretation of something that happened in the anime-at the end of the Sinnoh league, Ash faces a trainer called Tobias who has a Darkrai (also a Latios, and four Pokemon we never see). I don’t know for sure, but I suspect the episode was highly viewed (even for a league episode), however I do know that the character is highly polarizing-some see him as a great opponent, others as a cheap plot device for Ash to lose “plausibly” in a single episode so the next anime generation could get underway. I know it’s kind of thin, but part of me just can’t shake the idea that they may have learned the wrong lesson and that there’s a connection.