This isn't too far from my position on it, I think. This is one of multiple elements that are meant to encourage social play, and you can presume that the standard intended way of playing uses that instead of demanding multiple purchases.
I don't think people who view the two versions as a scam are wrong per se, but that "scam" is also predicated entirely on you both feeling an obligation to get the rather meager content that's split between the two versions and also being unwilling or unable to engage in the social activity that alleviates the issue. In high school, I just coordinated with my friends and we got different versions. Nowadays I might have to use online features if I didn't just shrug off the "missing" content.
So the problem's predicated entirely on the buyer's personality and behaviours. Does that mean Game Freak shares no fault? On the contrary, I think there's a lot of similar ways that games attempt to make more revenue by exploiting the gaming population's common obsessive need to have everything. That's why there are multiple more expensive versions of many games that offer more content or goodies. That's what the whole gacha game business is build around. The latter particularly preys on things like addictive personalities - for someone like me who is quite distant from that, I can play multiple gacha games and never feel a great urge to spent anything at all, but others can bankrupt themselves.
It's possible in that way to argue that Pokemon's two versions is a potential means to exploit people who approach purchasing a game in a particular way. But I kind of find it hard to get too upset about it when, unlike some other versions of this, it can be alleviated other ways such as trading with friends. Additionally, it has a cap of sorts - you don't keep getting more multiple version benefits for buying more than two games - which makes it significantly less alarming than with gacha games, which are designed to encourage uncapped spending from people with similar purchasing habits.
Having a single "version" in stores with an in-game toggle upon creating a new save file would be better, I think, but I don't think it makes as big of a difference as it's presented here, honestly. It doesn't do much to alleviate the behaviour of obsessively needing to buy the game a second time to get the additional content. I actually wonder if it might increase the cost of producing the game since you'd only be making a single totally uniform product.