The most common questions I get as an instructor always have something to do with the differences and similarities between Pilates and yoga. Pilates and yoga are often thrown around together in the whole mind-body fitness category, so I get the confusion. The short answer is, they have similar goals but they go about them in they're own ways. The connection of mind, body, and breath is at the foundation of both. There is a rhythm in both practices. Both can be therapeutic or incredibly challenging and athletic. And many of the postures/positions are even the same.
Still, I find that most people prefer one over the other. I find there is a deeper meditation that is achieved in yoga and an earthiness. Being done only on the mat with your own body weight, there is important weight bearing strength and stability built. Many of the releasing postures can take you deeper than Pilates simply because they are often held longer and are more dynamic. If you get a nice flow going, you can get the heart rate elevated for a completely well-rounded experience.
In Pilates, we always start with the deepest, most subtle muscular connections to create a stable foundation and deep mental connection to what is happening in the body. The alignment is universally applied for healthier movement of all kinds. The core and specific, targeted work in Pilates is really unparalleled (getting all the nooks and crannies), especially for those with limitations or injuries. On the equipment you work with spring resistance as well as your body weight, so it's a really unique experience with fast results. And the jump board is Pilates' tool to get the heart rate up for some low-impact cardio.
Being a Vinyasa yoga practitioner, myself, I am a huge advocate of both, especially together. Because much of what you do in yoga involves going into deep, dynamic postures and utilizing many muscle groups at the same time, it's important to have the foundation of strength and alignment that comes from Pilates. And because Pilates involves a lot of movement, yoga is a nice counterpart; the stillness, holding postures. Pilates also offers endless variety, while yoga can be quite repetitive. It's important to keep the body guessing. Mentally they take you to different places, keeping things fresh. And getting into a routine where you are practicing both, is like winning the jackpot. It's the best way to work towards complete, mind-body fitness.
Finally, the most important thing with all of this is that you find the right studio/style/pace/instructor for you. There are so many options out there and finding the right option for you makes all the difference in the world. In both Pilates and yoga, if you have injuries, there will be certain exercises/postures that you should definitely avoid or learn to modify. Both advocate mindfulness and listening to your body, the most important aspect of wellness.