Yeah, I kind of echo this statement. A problems with both Worlds of Darkness is the whole multiple global conspiracies from different splats occupying the same space. I'm not too sure about NWoD but the OWoD does run into that problem several times with things like the Camarilla, Pentex and the Technocracy. They've tried to explain it away and while it works some times, others are just more headscratchers. Mostly with Pentex though because the Wyrm and just how goddamn evil the mega-corporation can be.
The basic idea of a Pentex makes sense in every gameline where spirits are important (well, except Wraith and Orpheus, because wrong kinds of spirits). It in fact makes sense at both a Doylist and Watsonian level. On a Watsonian level, spirit want to fulfill their nature, to expand or realize what they are. It isn't on quite the same level as the nWoD spirits, but most spirits are primal things that have needs and wants free from the moral considerations of man.
That the spirits of pollution, of monopoly, of patronage and backdoor deals would influence the world through corporations and businesses is... pretty damn natural. They are born in such places, feed and grow there. It's the locus of their influence. But Pentex itself unifies what should be a dozen power-players into one mega-cult that doesn't work the moment you look at it too closely, and it's too tied to the werewolf interpretation of what the cosmos looks like, and to the Werewolf need for armies of disposable mooks.
On a Doylist level they show how fundmental and deep the rot goes, how not only is the world failing and falling, but that the fall is feeding itself. Corruption (of a human sort) begetting corruption (of a mystical sort) begetting corruption (of a human sort). So long as there is profit to be made humans will sell
deadly tainted medicine for profit. It requires no supernatural intervention for first world companies to sell pesticides that are also deadly carcinogens to third world countries. The blood diamond trade.
And part of the heart of every World of Darkness game is... the Darkness. Things spiraling downwards, things getting worse, the symptom covered up while the causes fester. Fighting corruption and pollution by fighting Corruption spirits and Pollution spirits that have gotten into bed with corporate fat cats fits. Unfortunately, Pentex itself takes up that entire memespace so even though they're only one (rather bad) take on this premise, they're also the only game in town.
Though frankly the nWoD is just as bad when it introduces villainous corporations. We have new ones in Hunter, Mummy, and Demon, and while the boxing of the gamelines keeps them from growing as bad as Pentex, they still are single player rather then a class of players.