We have a floor in our unfinished basement that is lumpy. They only poured 2-3 inches of concrete in the basements on our block back then. Our bungalow, we determined from permits, was built in the winter, on clay soil - so water absorption is not very good. Our theory is that that the concrete and soil below froze during construction, causing the ground to heave and crack the thin concrete in spots. We have repaired sections though out our basement.
I have seen bungalow rehabs where they remove ALL the concrete in the basement, dig down a little further, and add the right depth of new concrete. That might be the better way to go, as you need a solid foundation for your project. At least you could rest assured that you would not have problems down the road after you put money into a remodel.