Tick Tock Tick Tock...Joe? Your SGU fans are waiting for that news you said you would have for them.

[Hyndara]

As far as I know the story is the complete opposite. JM doesn't like JF. Well, I think after years working together JF began to feel the same way. He never mentioned an exact name when he is talking about the SGA-franchise. Sentences like "franchise failed because of some big egos" aren't a real evidence that he meant JM with it.
All I know, and I do not remember where I've got this information from, is that JM once told about the possibility that Sheppard isn't longer located in Atlantis in his Extincion-script (so this script is not only a daydream).

 

[stclare]

I cant speak for anyone specificaly my my take was that it comes from a combination of different little things. But like Hyndara, I thought it was more JM not liking JF. the big gripe seems to be that JM left Joe Flan off the end of season 5 video tibute/goodbye thing he did. all the main cast were featured apart from Joe. I would have given him an out if, JF had not been there when the video was made but Joe F was in a clip he used for the DH thankyou part. So he could have as easily mentioned Joe.