4. Bruce Banner Controlling The Hulk
When the Avengers movie came around, Bruce Banner had obviously spent a lot of time away from anybody with any interest in the Hulk and, in the final battle, he showed that had learned to turn in to the Hulk voluntarily in order to use it as a valuable weapon against evil. Not only was it not really shown or explained how he came to learn to do this, but he also previously turned in to the Hulk involuntarily whilst aboard SHIELD's helicarrier. This left two major questions: 1) How did he learn to control the Hulk? 2) Why couldn't he control it on board the helicarrier? It's a major issue that really did need more exploration and explanation.