Hi - I haven't taken a Pilates class so I can't speak to that, but I could definitely say that practicing yoga daily or at least several times a week will definitely get/keep you in good shape. There are lots of different types and levels of yoga classes, so you'll want one that will get your heart rate up for aerobic benefits. Look for a style that says it has "flow", or anything Ashtanga, or just ask your local yoga school and instructors what style would be best for your level and your goals. You can get a lot of weight-bearing poses in yoga that will really increase your muscle mass and strength, and this will burn more body fat for you as well.
Talk to any instructor about your neck injury. There will be certain poses they won't want you to do at all, and for other poses there will be modifications for you. But this shouldn't prevent a yoga practice completely.
You might just take a few yoga and Pilates classes and see what you prefer, or just mix and match.
- Heather
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Re: Pilates or Yoga? question for Yoga teacher or anyone
