I'm also going to say yoga. Yoga combines the best of cardiovascular fitness, strength, balance, stamina, flexibility, mental focus and core stability. There is much more to yoga than just postures or asanas and you can take it a far or as deep as you would like. Yoga is also very portable and you can do it anywhere and anytime.
To my knowledge Pilates, which can be amazingly beneficial, is primary focused on core strength and stability as the means to strengthen your body and provide flexibility. It is not as readily available and it is hard to do reformer workouts at home on your own because of the equipment requirements.