Differences between pulling power of Thomas trains

Part of it could simply be if the engine has been 'run in', often electric motor characteristics change as they are run and gain age, if done right the older ones can run smoother than an out of the box model.

However in this case it is likely to be down to as you quite rightly say gearing, different engine/gearbox designs favour speed and/or pulling performance. Also it could come down to the amount of weight added to the locomotives, a lot of the older ones have quite a few heavy metal weights in them do the current models have as much? This would affect speed and traction quite a lot...