@boynerdgeek: He is Professor Zoom. He has come to the past to make sure Barry lives a long and productive life as the flash so he can build up enough speed force energy to use it in the future. Thats why he knows so much about future Flash. In the season finale him and Barry go back in time with him killing Barry's mom and Barry trying to save her. He is the man in the lighting.
This issue has been brought up in multiple story lines. Cap isn't on the team because he is the most powerful or the smartest. He is the heart and soul of the team. He is the leader. He is the moral center. He has the tactical mind to come up with the plans of attack. He can inspire others to be better just by being around him. Not to mention because of his Super Soldier Serum he is more powerful than Batman and his shield is the perfect counter to a lot of powerful attacks so he is plenty useful in a fight. However, above and beyond all of that is his persona and his character. He is looked up to and respected by everyone. He has a voice that can and does command gods. In the middle of a fight you want a leader you can trust completely and won't hesitate to do whatever they say. When a man gives commands and Thor listens you don't question his right to lead let alone be on a team. Here is a good article about it http://www.comicsprofessor.com/2011/04/a-voice-that-could-command-a-god-captain-america-and-the-stoics.html