These coupling rods with the hollow cylinders were produced by TOMY before they got the Thomas license. The first character to use them was Henry, and they were reused for Gordon along with other aspects of Henry's design. It was carried over to the HiT Toys and early Fisher Price eras and the rods were even reused for Hiro. My three FP Talking engines (including Gordon) were the original releases without the punched wheels, and they were updated when the sticks were added to the boxes in mid-late 2011. On another note, the Talking engines with the holes move right after being switched on while the previous versions wait for the button to be pressed. Personally, I too think the non punched wheels are superior.
Thanks for the info Da-lag