I do love bodyweight exercises, but you do need to add some weight - like handhelds when doing squats for example. Pushups are hard for me no matter what so I don't need to add weight there, but I'm guessing you could add a weight belt?
I think the idea of doing both is a good one - do some heavy lifting and keep your flexibility up. Pilates and yoga don't isolate muscles - they use your whole body, so it is balancing.