Tom Cruise spends pleanty of time with Connor and always had. Bella not so much. To say Bella has moved in with her boyfriend so can find her own way now is, in my mind, incredibly cold and unfeeling. Girls need their mother too and I don't believe Cruise's sister provided the love and support daughters need from their mother.
Bella is overweight and has been for some time - to me that suggests she is unhappy and using food as a comfort. I'm entitled to express that opinion here and I think it's relevant. She was separated from her mother and I believe that has had a damaging on her development.
Bella & Conor's childhood development was probably warped by the fact that their father was constantly away from their for long periods of time due to his film shooting schedule on distant locations. It seems, however, and photos over the years, show that he tried to be a responsible father despite the demands of his movie career. He had his sisters assist in taking care of them & home schooling them when he was away.
I don't know the relationship Bella has with Nicole. In some reports, Nicole, allegedly claimed, the kids turned against her to stay with their father, then there were reports that Bella felt neglected & wanted to go live with Nicole. I agree that Bella's weight gain probably had alot to do with her emotional issues with her parents, and perhaps, the feeling she felt neglected.
Her emotional state could have been hurt. too, when Tom married Katie, and when they had Suri. The "evil stepmother" syndrome happens alot when a remarriage takes place, and less time & focus is spent with a dependent child. Bella could have suffered some jealousy when Suri was born, because Tom spent more time doting on her and less on Bella who was in her teens.
I remember all the media stories that came after Tom & Nicole's divorce & how she allowed Tom to take primary custody of the kids. In child custody cases, the mother usually is granted primary custody. Nicole did not want it & was focused on her movie career. I think with Bella, the daughter in the relationship, this may have led to feelings of abandonment. But, I'm speculating.