Fortunately, all other things are NOT equal.
Simply, a 2.5' drive has less room for error. If all other things were equal, a 3.5' drive would be more reliable, mainly because the engineering tolerances are so much tighter in the smaller drive. Thermal management tends to be more important for 2.5' drives because of the smaller heat sink, but also because the air flow around the drive in a notebook computer will tend to be less than in a desktop computer where 3.5' HDDs tend to be deployed. On the other hand, the bigger drive has more mass in which to sink heat, so it's a bit of a wash.
I think it's safe to say that because a 3.5' drive is moving significantly more mass (bigger and more disks, bigger motor, bigger head stack) than a 2.5' drive, the 3.5' will generate more heat due to friction. Air friction is probably not as important as good ol' mechanical friction.
