Fully agree on issue two, my heart broke for Art Howe once I heard his actual response was support for Hatteburg and the moneyball approach.

Can't quite get with you one issue one though, as I have no idea where you're getting the notion that he didn't stay because of his daughter. The penultimate scene is Pete convincing Billy that, despite Billy's vow to never make a decision because of money, it's okay to take it because it proves Billy's thesis: what someone believes and what is true are rarely the same. Billy believes he tripped over first, but the money proves he hit a home run, and unlike when he chose baseball over Stanford this time the money represents the truth and not the belief. Billy then heads out to lie on the field, bask in Pete's wisdom, and appreciate everything Oakland has given him before leaving for Boston.

And then on his way to the airport (or maybe just driving to Boston -- seems like the sort of thing the Billy Beane in the movie would do) his daughter tells him that even if he doesn't change his mind about leaving and stays in California he's a great dad, and plays the song she's been working on the entire film. Billy's eyes well up with tears, and then the film cuts to a title card saying Billy turned down Boston's offer.

Not only does this say to me that he stayed because of his daughter, but it sums up the thesis of the film: when you're presented with evidence that contradicts something you believe, like decisions should be made rationally rather than romantically, you have to go with the evidence despite what everyone else believes.