Although I am currently not involved in running a minyan, having taught in various schools across the hashkafic spectrum, I am quite familiar with how tefila is conducted. It seems to me that before we can evaluate how students are performing in tefila, we must educate them on how to do so. Just as I can not expect my students to know how to read a gemara without first giving them the skills, it would be naive for us to expect our students to know how to pray properly, without teaching them how to do so.
My suggestion is that we move from minyan as just a time to daven to minyan as a lab for tefila. If there was a class on tefilla, including why we pray, why praying is necessary and similar issues, we would begin to tackle the problem. Instead, in most schools, we tackle the how; when to stand, what to say and how to bow. Perhaps some beiur tefilla could be included in this class, but I do not believe that the main problem is a lack of understanding of the words. I am well aware of my own struggles with tefila despite a grasp of the meaning of the words.
To be sure, the class would only be a beginning. There would also be a need for students to be able to express themselves about their struggles, successes and thoughts on tefila, perhaps through a blog and/or a brief thought before or after minyan.
Finally, and perhaps this is most crucial, we need the adults running the minyan to open up to the students a bit about their own struggles and successes with tefila.
If we treat tefilla as a part of the educational part of the day, where we try to reach the student intellectually, emotionally and spiritually, we have a chance to achieve something. If not, we will at best create robots who look like they are praying, and at worst continue to fail to touch our students lives in this important area.