To make Yao Ming pack in the paint, and runs less, aka zone defense, is only effective against a hand full teams. Nowadays, with everyone packing out of the arc shooting 3s, zone defense is the worst thing you can have. Since zone doesn't work, we only have a mixed man-on-man. Once Rockets does that, opposite teams will run Pick and Roll with their guard and center. To cover his man, Yao has to come out and challenge. Once it's rolling, Yao has to show up on the guard, that's not JVG asks Yao to chase guards, but the only way to play against PnR.
You may argue why Shaq does a lot less show. That problem is two sided.
One, PF in Miami and old Lakers does dirty works, they switch with Shaq in those occasions. Howard, Swift don't do that. Howard is too slow, and Swift is too dumb, Hayes is too short and foul-prone, which leaves poor Yao out there.
Two, although Yao is putting up better numbers than Shaq is now, Shaq is still much more intimatating than Yao is. It takes lots of risk and courage for guards to drive against Shaq, because he may end your career. Shaq doesn't necessary do that, but the fear is there. Yao doesn't deliver that pressure. He will alter/block shot, and try to stop you, but you can also try to score on him or draw fouls on him. Every guard knows exactly that Yao wouldn't hurt them, and only try to avoid the foul. Shaq doesn't do that. He will stop you with all means, to show you that is his territory. Until Yao starts to swing some elbows, and put his 300 lbs on Parker like players, he will face attacks from guards every night.
Again, it's not JVG's system, which worked pretty well last year, and it wasn't executed properly due to personnel this year. Some people say that coach should design a system according to his players. Yes, the system was designed for Yao and TMac, not for Bogans, Swift and Head. Triangle or Princeton, PJ or Pop, if you are forced to play Yao + 3 NBDLers, you will lose.
Pleasure in disguise this season, Yao took the opportunity to re-discover himself.