maybe some sort of plumbing or vent? could you use as a desk or bookshelves?

I have a random indentation in my master bedroom. Mine appears to be the result of the architect having to make the wall line up with a tub in the master bathroom on the other side. What's on the other side?

It almost looks like shallow closets or maybe they were put there for custom cabinetry that is no longer there.

As for designing around it, you could put any dressers you have in the indented places. If you only have one, I would buy another one and you will have more storage!

Make them go away. By the time you decorate "around" them, they could be gone for a fraction of the cost.

I can't see the rest of the room, or tell the depth of the dips -- but perhaps putting shelving custom cut to fit, moulding and accent paint to the back, it could look amazing. Although the idea to just make it go away by hanging a drywall is an alternative. Hire a carpenter to give you a quote for both -- and if you feel like being creative, you could keep them and if you don't get rid of them. If it were me, I would see if I could do something there. I actually like spaces like that. I just searched shelving in niches and saw some great photos for inspiration...http://www.houzz.com/photos/query/custom-shelving-in-niche-bedroom