Let's be honest here. There's a reason all the old guys who came out of jail, or even Junior, couldn't respect him. He was a punk. He ran his crew with no discipline. For example, when Chrissy was a nothing, an errand boy, back in '95, he was allowed to interrupt two made guys talking (Tony and Puss) about Family business.
Chris was Tony's protege. This gave him a longer leash to break protocol.
When Richie took down Beansie (the first time), Beansie was right. The guy had a right to earn. What does Tony do? Instead of having a sitdown and taxing Richie for not coming to him first, and telling Beansie to kick up to Richie, he instead comes down hard on Richie, and doesn't give him anything. He sides with a civilian over an established wiseguy, a skipper.
Tony launders money through Beansie's restaurant, which is why he didn't want any hot headed gangster confrontations in the place like the one Richie had with Beansie.
Make no mistake, Richie went into that place to challenge Tony's authority. He used Beansie's debt as a technicality. It was out of line for Richie to show up to one of Tony's restaurants with that attitude.
He lets Davey Scatino walk scott free from Richie, again siding with a civilian, when Richie is in the right - Davey already owes Richie money, and he's playing in the Executive Game?
It was a tax. Again, Richie going Little Caesar right in front of important civilian clientele, among them Frank Sinatra Jr. That game is more important than Richie's petty beef with Scatino, which was also a challenge to Tony. I doubt Richie came down that hard on other people who were behind in payments. He was hoping to get a response from Tony.
He treats Feech with contempt and takes a heavy handed approach to a guy who was a living legend.
Feech's heist at the wedding of Dr. Fried's daughter was his death certificate. Freid was with Tony.
He bumps Christopher, newly made, over Patsy, a well established made guy.
Chris was his protege. Small boats rise with the tide. Patsy's borderline treachery after his brother's death didn't help. He's lucky Tony didn't catch him pissing in the pool.
He bumps Gigi, a soldier in his crew, up to Capo of the Aprile crew, even though Ralph is the more qualified, better earning guy and has the respect of the Aprile soldiers - purely out of dislike for Ralph.
As he told Ralph, he wanted someone he could trust.
Let's be honest here. For as interesting as Tony was as a protagonist, in Mafia terms, he was a Punk. A disgrace. He only made it as far as he did because of his father, and because no one else wanted to be Boss.
He made money for John Sac and Carmine Sr. It's a business. Tony understood that. The mooks you're defending did not.
