I agree, Bobby would have made a good boss. Tony always talked about how whacking guys could hurt the family and how he wanted to run the family as a business but he was always the first to lose his temper and violate his or LCN rules. It's what made Tony a great CHARACTER but not that great a boss. I think back to when Tony called Chris to the bakery parking lot at night to tell Chris that he would be giving orders through him and Silvio. Tony spoke of bringing the family into the 21st Century to which Chris replied "we're already in the 21st Century". To me that summed up Tony's management style - two steps forward one step back.
I think Bobby would have really brought about changes that would help to reduce the familys presence on FBI radar and he would have been less focused on petty BS and more on the bottom line. Bobby wasn't scared to use violence but I think he knew it should be reserved as a last resort. When it was confirmed that Vito was gay it was Bobby who was hesitant about taking any permanent action suggesting that he be banned from the "social club". Also Bobby never got involved with a goomar which left him more clear headed than Tony. The other thing that impressed me about Bobby was his patience. He'd put up with Uncle Junior and Tony with all their snide remarks - it might have pissed him off and he'd mutter something under his breath but he knew how to pick his battles. Finally, Bobby would have been a tough competitor against New York and Phil knew that hence ordering the hit on him instead of Paulie.
"I suppose. Who the fuck really knows? Still, it's nice to think that"