Game Freak builds their games with Doubles and Singles in mind. Doubles is the "official" way to play soley because of the VGCs. (Although MLG had a Pro Curcuit for Singles for DPP iirc and has an on-going 6v6 Singles Ladder for B/W.)
Saying that Game Freak only "balances" the game for Doubles is calling them blind. Game Freak knows EXACTLY why Diamond & Pearl revitalized the series. Wifi. They know it definitely wasn't Double Battles. And, as a budding game designer myself that knows the industry, I can tell you that, just like how we do with PO, they can extract data from their servers and look at it to go "Okay, what are the most popular things we're seeing here?" When they look at the unrated friend battles being 90% 6v6 Singles, then they know what to focus on.
The VGCs are not run by Game Freak. The VGCs are vastly just a PR stunt held by the marketing division that advertises Pokemon Merchandise and is also responsible for the Pokemon TCG tourneys to....advertise Pokemon more! What a shock!
If I have one gripe with gamers, it's that you don't give game developers enough credit. Smogon is small. PO is small. BUT Game Freak knows we exist all because of one thing, there is no big, competitive Pokemon site of Japan. If you search competitive Pokemon in Japanese, the first 2 results are Smogon with the 3rd being a question asking why competitive Pokemon is so popular in North America. Does Game Freak care about our rulesets or ban-lists? Hell no. Are they aware that there is a community 116,000 strong on a site vastly dedicated to 6v6 Single play? Absolutely. It's Game Freak's job to know the community. It's bad game design to not look for easily find-able sites like Smogon the specialize in YOUR game.
Game Freak knows their fan-base. They know how much we love 6v6 battles. But they also know that 6v6 ranked matches are a terrible idea. They know that not everyone has an hour to spare for stall, but they also know that players will try to stall the timer if they have the lead if they implemented a 30-minute timer into 6v6 battles. They chose 3v3 & 4v4 because they go fast. The term "snack gaming" gets thrown around a lot, but that's what it is; most people only play Pokemon for 10, 20, 30 minutes a day. 3v3 or 4v4 battle rarely last over 5 or 10 minutes. That why Game Freak chose them. No one wants to lose points on a ladder because they can't keep playing for another 40 minutes.
Game Freak balances the game for 6v6 singles and 4v4 doubles. The game was always about 6v6 singles since Red & Green. They started "balancing" the game with Gold & Silver because then knew that they have made a competitive game series now. The series was balanced for singles every game. Up until the VGCs started in 2009, there was no question about that. You don't take a game series with 5 generations of installments, all built for singles play and then turn it into a purely doubles-balanced game. It doesn't work that way. No matter how much VGC players wish otherwise, they will always be in the back seat in Game Freak's designing process.
tl;dr: Give Game Freak the credit they deserve.