I completely understand this feeling. Even in middle school, we performed investigations that had to be carried out in a specific way--students had to follow given directions. In these kinds of labs, I worked hard to make some part of the lab open for student planning, but I was not always successful.
This weekend, though, I had an epiphany. What if the investigation went something like this. . .
In the course of a phenomena-based unit, as students are working to gather information to figure out a phenomenon, there arises a need for a specific kind of data. For example, in the Next Generation Storyline unit I'm using, students are currently trying to figure out what happens to glucose when it leaves the chloroplast. The next investigation has students analyze various parts of the plant/tree for sugar, starch, and cellulose. These tests use specific reagents and have specific procedures. Students cannot be expected to design the procedures for these tests. However, when students realize that they need this data, the teacher can provide a procedure that will give the students the data that they have requested. It's a very simple switch. Instead of saying, "Here's the next activity we're going to do." Students drive the learning and make suggestions about what to do next or what they want to learn next. These suggestions should eventually circle around to something like, "I wonder if we would find glucose in certain parts of plants/trees?" I can then follow up with, "Well, I have some specific tests that show the presence of simple sugars, starch, and cellulose. Would those help you in trying to figure this out?"
In this method, students aren't designing a classic science fair investigation from start to finish, but they are providing the need for data, deciding how to use the specific procedure to acquire that data, and deciding what to do with the data that they gather. In doing this, they are "doing what scientists do" and "thinking like scientists."
This can't be the only kind of planning and carrying out investigations that students do. The details of the practice (found in Appendix F) provide more information on everything students are expected to do with regards to planning and carrying out investigations in each grade band. However, this is one more way that we can move a little closer towards the vision of the NGSS in our classrooms. Is there a lab in your future that you could try this approach with?