I compared my 2011 EC125 frame with a EC300 and the difference is only the stearing angle and the lower pipes below the motor. The mainframe ist NOT smaller than the EC300 one. The biggest difference between the 125 and the 300 is the weight of the engine. The 125 motor is about 15lbs to 20lbs less. This makes the big difference in the handling.
Yes I know that, but the point is the older frame starts out smaller for the 250/300, so it seems more correct for the 125. I like the new frame but lets face it it was designed as a 250/300 and will be heavy 125.
The swingarm is likely hiding a couple pounds, but my guess is that you're right about the engine being a prime target.
It's amazing where you can save weight while improving function - the new AXP poly skid plate is almost a pound lighter than the aluminum piece it replaces.