I take issue with a couple of points:
1) no particular team is just better conditioned than another, that is just myth. Every coach works on conditioning at every practice.
2) you expend more energy playing defense than you do on offense, so the high octane offense doesn't explain better conditioning.
3) some players, genetically, have better endurance than others. The coach can run the legs off some players in practice every day, and they still won't have the endurance of another player.
4) some players, and teams, have the will to gut it out in the second half, when they're tired, their legs are tired, their lungs are burning, but they still expend extra energy.
5) all players tend to shoot worse near the end of games, not because their lungs are tired, but because their legs are tired--it affects their shot, so they miss more shots.
6) some games seem to be played at a faster or slower pace only because the refs don't call any fouls, there are few play stopping whistles, and the game flies by, failing to give players multiple moments of rest. Other games, many fouls are called, lots of timeouts, turnovers, play stoppages--this gives the players lots of good, short rests.