The Movie: Every species we come across in the Star Trek universe is humanoid. This is not unique to Star Trek: Into Darkness; it's a hilariously campy part of the franchise as a whole. Need an alien? Chuck a weird rippled forehead on it and you're done. Though the recent film series has not mentioned why this incredible cross-planetary coincidence occurred, apparently it has been explained away in the past as being the result of some ancient Humanoid race which seeded genetically-engineered cells on multiple worlds that guide evolution towards the humanoid template.
Real Life: Oh my God, it's like Prometheus all over again. You cannot "guide" evolution on such an enormous scale — only the universe can do that. Are you the universe? No? Then stick to breeding wolves into pugs over thousands of years, because that's about as much evolutionary power as humanity has been able to muster so far. The real problem with the idea that evolution must lead to a humanoid structure is the egotism of it, as if the human body is the greatest design ever. Oh really? More awesome than a T-Rex, or a Great White Shark? Are humans better than Water Bears, microbes that can become spaceships if they want to? I think not. There are many ways to achieve evolutionary success; that is the powerful beauty of it.
In fact, it could be argued that humans are less successful because we do not live in harmony with our environment at all, raising all sorts of doubts about our ability to survive long-term. What good is this awesome brain we've developed if we can't even use it to protect our descendants? Humans are not the evolutionary endgame: there is no evolutionary endgame. And like Prometheus, the deification of humanoids does not explain what all those billions of creatures that have called Earth home are for... decoration? It seems humanity has a species-wide case of Narcissistic Personality Disorder.