I love hearing this. The easiest way to show a patient that mobility and stretching are not the same is to test for a tight hip flexor, stretch it out for 3 minutes, show the difference on a test, then ask the patient to walk around for a few paces. Bam, hip flexor is tight again. But we just stretched it out!
That's because your muscles don't regulate how tight they get to be. Officially that is not entirely true, they do contribute but that's not the point I am making here. What I am saying is that it is your brain that determines how tight your muscles get to be. Via reflexes and nerve potentials and a bunch of nerdy things that basically say if you don't make your body use and feel a muscles in it's lengthened position, it will not work there. It will be tight. ....Huh?
Muscles move bones, if muscles move bones in a certain motion they will improve their ability to perform that motion. We are efficient beings and that is advantageous. Also efficient, if muscles do NOT move bones through a motion, they do NOT move them very well there. Forcing yourself into a position you don't move into very often, also known as a stretch, will only last until you need to move out of it and through a different range of motion again. Then you fire up your old pattern (your nerves activate your muscles) and your efficient muscle behavior returns.
The answer to this conundrum is to train. Train the little stuff (posterior pelvic tilts, hip shifts, shoulder rotation, scapular rotation, rib cage rotation, ankle dorsiflexion, ankle eversion) and then use it in big patterns (squats, deadlifts, push-ups, pull-ups). Then you will teach your brain, muscles, and body how to be energy efficient in this new range of motion.
How do you know that little stuff needs to be trained? That is not as easy to say. At least not in blog form without having ever met you. Specific tests, performed in clusters, provide a systematic understanding of how someone likes to move in order to be efficient. From there, specific exercises can be prescribed on how to improve your efficiency during the movements your body does not perform so well. There are many schools of thought on how to do this, but I promise you it does not start with ultrasound and end with an ice-pack and some e-stim. Unless you like that stuff. I didn't NEED ice cream to get better at T-Ball, but you bet your ass I love ice cream and am more than willing to play as much T-ball as it takes to get it. Although, I am not the greatest baseball player....