The newer Series 4 has double the storage (16GB) of the Series 2 (8GB), so it would naturally have more free space.
The WatchOS would be a different configuration between those 2 models, and S2 architecture is 32-bit, where the S4 is 64-bit. That would account for the difference of a system space used (in your example) with 2.8GB on the S2, and 3.5GB on the S4.