I compared my old and new Thomas sets, and here are my findings.
I own the original release of that set (from late '90s or early 2000s) and the latest release (bought in 2018). I think I bought the original one from Rainbow Ten (a hobby store in Japan which also did some online business). The set still has a price sticker in Japanese yen.
The packaging has changed between the releases. Original release's box was larger and has a Styrofoam cradle vs. cardboard cradle in the new set. Even the part number is different.


Next, the locomotive itself. The original mechanism uses a fairly primitive large motor with open frame and top-mounted magnet. Current is picked up by metal wipers contacting the wheel treads.

All the drivers are geared, using external exposed gears (like it was done on some early N scale models). The driver axles also ride directly in the solid diecast frame - no separate bearings.

This older model runs ok, but not great.
I also found it interesting that the face molding was reworked on the new model. Not just different paint, but the face itself is slightly different.

This photo shows the difference in the chassis. The new model has a split frame and uses a low-end coreless motor (with a flywheel). Original model had no flywheel.

This photo shows the differences in the drive train construction. The new version has the driver axles mounted in brass bearings (typical design for most currently made steam locos). It has no pickup wipers. Instead it picks up the electricity through the driver axles and bearings. The new loco also has all the gears enclosed inside the chassis, and the gears have finer tooth pitch. This, along with a coreless motor and flywheel results in much better performance. Also worth noting is that the new loco has wheels with narrower tread and finer flanges. Basically it has the same attributes as other contemporary models of steam locos.
I also noticed that the shape of the buffer bases has changed on the new model.

Looking at the other info in this thread, it appears that there were at least 3 iterations of this model.
1. The original with crude motor, pickup wipers and external gears.
2. (Mike's model shown earlier) A split-frame chassis with brass bearings, fine enclosed gearing, and no pickup wipers. But that iteration uses a standard motor.
3. My latest purchase. It is pretty much the 2nd version retrofitted with a coreless motor.