@RayKray
Machines very much isolate muscles and can force you in to an unnatural range of motion (which is not good when you are hypermobile and already have a less than natural range of motion).
On the other hand free weights not only hit the main muscle but also work other muscles including the little stabilising muscles around the joints.
And compound lifting (bench, squat, clean and press, overhead press, deadlift, rows, etc) work many muscles at once, including the core. For example bench will work chest, shoulders and triceps. Deadlifts work hamstrings, glutes and back. Squats (depending on style and depth), work quads and glutes.
Then explosive lifts such as power and hang cleans, work the muscles in a different way, there's a great crossover to improving things like running and jumping. Plus they give you quite the cardio workout.
The only machines I use are the lat pull down assisted pull up and seated row. (I also do kneeling lat pull downs with the cable machine). For everything else I use a mix of barbells, dumbbells and Kettlewell along with a trx.
I also do a mix of heavy compound lifts, lighter accessory lifts and explosive complexes.