I get in trouble every time I comment on John's theology publicly, so I'll be circumspect, but folks have criticized the following in JMF's theology:
1. His definition of theology (as application) (though this has precedent in Ames and Edwards),
2. His theological method ("tri-perspectivalism"),
3. His claim that we can know God "in himself," (not something the Reformed have taught),
4. His claim that God is both one person and three persons,
5. His application of the RPW to every area of life so that it ceases to have a distinct function in regulating worship,
6. His criticism/rejection of the traditional/confessional application of the 2nd commandment to pictures of God the Son incarnate,
7. His criticism/rejection/revision of the traditional Protestant law/gospel distinction and his support for elements of Norm Shepherd's doctrine of justification and apparent support for the FV.
He has written widely on theological method (he has a new intro to theology out), on apologetics, the doctrine of God, worship and ecumenics.
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