Tony broke pretty much all major mob rules and Phil didn't really do anything against the LCN code of honour. Tony was a rat (he ratted out Feech LeManna, a stand up guy who did his time, and a couple of Muslims), was seeing a shrink and had affairs with other made guys' women.

Overall IMO Tony was a horrible boss. He killed some of his top guys and earners for minor things while he was harbouring Chrissy and Tony B (eventually through time he realised his mistake and killed them both) to the resentment of the rest of the family. He was an insecure guy who was only respected by few guys from his original crew and those in the family who were younger than him. That's why guys like Richie, Ralphie, Feech and others often tested him and didn't really fear him. I doubt they would be pulling the same antics if a guy like Philly Leotardo was their boss. Just look what Tony turned the once prosperous family into. In season 6 their top earner is that old fart Carlo making 3 times less money than guys before him and they have a joke like Bobby as an Underboss. Compare that to the family he inherited, with 5 solid crews and plenty of earners. He more often than not treated his made guys like shit (with the exception of morons like Tony B, Chrissy and Bobby who were promoted) and would surely cooperate with the FBI if facing serious time (he had a good relationship with agent Harris already).

Phil was right about Tony, he stepped over his own uncle to become the boss. The war with NY was in many ways Tony's fault, he was testing Carmine's patience time and time again and told Johnny and Phil to go fuck themselves. Phil wasn't really boss material but was at least a respected stand up guy who did his time.

That said, I love Tony Soprano as a character in the show, but speaking from LCN perspective he wasn't a real mobster.