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One of the biggest difficulties with the lecture format is that it can be difficult for the lecturer to gauge whether or not the class is understanding the material. To remedy this, we should experiment with different methods for real-time feedback - clicker questions are one example, but we can try others. For instance, we could have something like political debate dials, where each student is given a dial which they can twist to "understanding" or "not understanding"; the lecturer would have a screen displaying how much of the class was understanding at any given point. An example: http://www.perceptionanalyzer.com/.
This is only one idea; MIT could easily hold a focus group of students to brainstorm many more.