Two things: I see a lot of somewhat blind respect for Subway and for locally-run and family-owned businesses. Of course, both have a dark side to them. People just like to blame the big corporations because they're much more visible, and people across the country or the world will know what they're talking about.
What people don't realize is that Subway was deliberately created to be cheap, small, and easy to set up. Subway is unique among the major fast food chains in that it has a division set up mainly to establish new restaurants, so much so that it has a stranglehold on the deli sandwich business. Over the past few years, Subway has had the strange situation if losing sales due to competition from other Subway restaurants too close to each other; that's how bad it's become. (Quizno's is at a distant second, whose sandwiches I prefer...maybe tenfold. If the Pokémon deal happened with Quizno's, it'd be a dream come true. For the record, Blimpie's is in 3rd, and Togo's is in 4th.) On the other hand, their $5 footlong, which, unlike Quizno's copycat deal, actually spans their entire menu, is very tempting.
Locally run businesses can sometimes be even more underhanded than the large companies. They have a reputation for being honest, sincere, and all that other jazz, which means they have a loyal consumer base. And what happens when you have a loyal consumer base? You're free to price-gouge. This can be seen all over Santa Cruz, California, where I'm at right now: There's such an intense hatred of the big corporations that these small businesses can do stuff like sell salads for $16. (This is no exaggeration.) People are loyal to these places and are willing to buy food at these ridiculous prices because the local businesses are scamming them. People place trust in these places that the businesspeople take full advantage of.
Anyway, the reason why Pokémon USA chose Burger King as their chain is because they had previously partnered before and thus Burger King would be the chain most willing. (This isn't to say that Nintendo and Burger King are an icon though, since Mario toys were previously distributed at McDonald's and Wendy's.) Scold them for their fatty foods as much as you want; it doesn't change the fact that a footlong tuna sandwich, even without the cheese, contains more fat than a Whopper.