I think McMahon has issues with JR because JR challenges Vince in some ways, and criticizes him for some of his choices. He doesn't always toe the company line, and calls things as he sees it in cases where that isn't the politically correct thing to do. He still gives McMahon loads of credit for all the good things he has done in the past and continues to do for the business, but will call him out via his blog or sometimes even on air when he thinks something is a bad idea. McMahon knows JR is good business, so he keeps him around, and I'm sure he has some appreciation for all JR has done for the WWE, but Vince's ego probably trumps all that in some instances.
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