I don't believe the reason why people picked Pinkie as pyro is not just because of Cupcakes or she's an arsonist (let's be honest neither is Spike, so that excuse could be used against almost every mane 6 cast). The reason why people picked Pinkie is because both Pinkie and Pyro act like children. Both their minds are child-like and they believe everything is happy, unless Pyro takes off his pyro goggles, or Pinkie opens her freakin' eyes and see the danger that is in front of her, or the dangers that both Pinkie and her friends are going to deal with (*cough* Dragonshy *cough*).
Another reason why people picked Applejack as Engineer is not just because she's a country pony like the Engineer himself, but the fact is that she is a known female character that rebuilds/build things. A great example. Her barn. Almost every season, her barn will be destroyed, and she and her brother Big Mac will be there to always rebuild it. And during the times she's not rebuilding, she's seen applebucking, and selling apples. True that she isn't the type of pony that could do math problem, but let's be honest, neither is Pinkie. In fact, if we think of one pony that is extremely good with math, Pinkie would be last in the list. Applejack rebuilding barns, fences, etc is similar to the Engineer building a sentry, dispenser and teleporters. Applejack's applebucking is similar to Engineer collecting metals. Applejack selling apples is similar to the Engineer's dispenser giving away ammo, health, and metal to his team. And that's why people choose her rather than Pinkie. But whatever floats your boat dude.