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You may have already found a solution to this problem, but I am currently doing the exact same thing, and I was encountering the exact same problem. I was also using the teb_local_planner, but it really didn't make sense that the local planner could be causing the waits. In the end I decided it was something in move_base, so I put together a very simplistic version of move_base where I monitor the global planner, local planner, and costmaps. This may not be the best answer for this problem as move_base has some nice features that I am missing, but I don't have it wait anymore when it reaches the waypoints and I also didn't need some of the other features in move_base as well. If you need some examples, look at NavfnROS and TrajectoryPlannerROS. I only suggested these planners because they have some examples of how to set it up, but you don't have to use those exact planners. You can use the global_planner and the teb_local_planner in a very similar way or even write your own.