I've never finished any larger project, but I'll try to reply anyway.
What tools are you guys using to track the engagement of your gamers?
I personally find it immoral, so I wouldn't use any kind of that tools.
How do you keep them motivated to play?
By trying to create an interesting experience.
What do you think would be a software/tool that would help you a lot in monitoring how satisfied are customers with your product and how engaged they are?
Brain scanning helmets, combined with a webcam that has to be kept always on during gaming. Maybe the game would only start once the player puts the helmet on and immediately stop if the helmet is put off or the camera obscured.