A cheaper controller would have made the Switch a better machine for a core enthusiast market. It would have dropped the price of the console and made it easier to get into games like Zelda and Mario -- arguably it would have even made them better by removing the temptation to screw them up with motion controls. It would have been even better for something like Mario Kart 8 Deluxe by dramatically lowering the barrier to entry for four-player gaming. But the surprisingly versatile Joy-Con seem like they're going to be at the center of expanding the Switch's capability while keeping the core console intact. Any console is already a platform, but the Joy-Cons are giving the Switch the potential to be a much broader platform than its competition.
Expensive Joy-Cons could have gone the other way. The Switch might have been compromised by a high price at launch if, say, Breath of the Wild wasn't as good as it was. But that's not the way things went down. Now that the Switch is here and killing it, the Joy-Cons are going to be Nintendo's best avenue towards accessing new uses and markets. And the fact that every Switch owner already has them means those new uses will be much easier to access.