IMO anyone would have trouble with the pace of the offense. I'm sure the players do get tired, and to a degree the Eagles players are less so because that's how they always practice. But ultimately that offense scored less points than the Cowboys offense did last year. The big issue with the offense IMO is the affect it has on his own defensive players. Chip runs his super fast offense and ignores time of possession, that means his defense is on the field more than half of every game. His defensive players wear out over the course of the season. Combine that with the fact that his defense might be out there for a long drive, then see the Eagles offense go 3 and out and actually end up back on the field in less than 2 minutes. They don't get any time to rest.
His defensive players start to suffer late in the season, when they are needed most. In high school and college that's not an issue, because rosters are huge and players are much more interchangeable. They haven't been weeded out yet to the degree that NFL players have. So he's got a small rotation of guys who are now extremely good at what they do, before he had a huge rotation of guys who were probably pretty good at what they did. So if he had to grab another guy from the roster and plug him in it probably didn't make a huge difference. Well now he's only got so many guys, and you can't just grab a guy and put him some place else. So when his guys start to wear down and get beat up over the course of the season he's left with guys who simply have to stay out there and perform, but not at the level they could if they were well rested.
As a result I can't see his team ever winning a Super Bowl. They'll get less efficient the longer the season is, and the competition will get tougher. The teams he's facing will be better prepared deep in the season, and an opposing DC knows he's only got to force a couple of three and outs to get the Eagles defense gassed. Chip has created what I think of as a sprint team - if the season was short it would be viable, which again is why it lends itself to college and high school.
Now I haven't talked at all about the X's and O's because frankly I don't know much about those things. I'll leave that stuff to somebody who knows more about it, but those are my opinions based on watching the Eagles under Chip.