Some teachers and parents I've seen have taken such software, monitored children's usage of it, and figure out how it fits with other kinds of learning that the student is doing, or how to help the children use those skills. Better still is software that assumes group interaction up front. By assuming that the humans in the room are doing the teaching and learning, the technology can be used for what it does well - organizing and presenting information. Students using this approach are much more likely to retain the facts that they discovered than the facts that they were just given. There are many kinds of tools for creating knowledge, ranging from general tools like word processors, paint programs like KidPix, and multimedia or web-page development packages, to specific tools for exploring physics or Autodesk's 3D Studio or Autosketch.
Most educational software seems to be developed as an extension of workbooks or television.
The packages I like are developed as extensions of paper, crayons, and cameras. As an erstwhile software designer I have always felt that if one needs to resort to the use of extrinsic motivation for a software environment to be educationally useful, then one has failed to make the intellectual content engaging in its own right. This is my view is an example of flawed design. There are many other examples. The essential point is that the designer must have a deep understanding of the subject as well as a deep understanding of the ways in which people do and do not develop understanding in that subject.