I think you can make a stronger case against powering up any given Pokemon than for it. Here are some reasons why you wouldn't power up the top three: Mewtwo is the best Psychic specialist but there's no use for Psychic specialists right now; with Shadow Ball it's a great generalist but the age of generalists is gone (also has few applications as a Ghost specialist); with Focus Blast it's more potion-efficient in gym attacking than Machamp but that's about it. Kyogre has been hyped for getting Origin Pulse soon and that should give players pause in powering up current Kyogres with Hydro Pump. Rayquaza is also a great generalist but has no specific use right now, and Dragonite performs almost as well as a Dragon-type attacker and doesn't require RC.
Power up what makes you happy. I'm not disagreeing with the claims in the article you linked, but I'm kind of tired of seeing all this discussion about what should and shouldn't be powered up. Dust doesn't go away if unused, so there's no harm in just waiting until a need arises to power any given Pokemon up.