SotC was the latest and greatest ... when it was released. It included all the upgrades Evil Hat had made to the system. Its SRD was the basis for a number of other "3rd edition FATE" games. Evil Hat themselves referred to the engine as FATE 3rd Edition from time to time, separately from the game it was in.
Evil Hat, however, are tinkerers. As they saw improvements, they themselves adopted and encouraged them.
Fate Core is newer, and many feel it's also improved, from the FATE 3E reference. It includes some streamlining, and a reduction in mechanical complexity (especially in handling of Stunts). It also has a new spur - the Fate Accelerated rules, which are for a different style of play using the same core concepts.
Note also - with the change to Fate Core as the flagship, so also is gone the all-caps name of the system.
Evil Hat even has a beautiful post which shows the 3 editions before Fate Core...
And it has a graphic... It shows two Fate 3 systems: SOTC and Dresden Files. (Other Fate 3 games are by other publishers.) It also shows that Evil Hat plans to revise Spirit of the Century to Fate Core, and Dresden Files to Fate Accelerated (which is under the Fate Core umbrella as a subset).
The graphic also explains (by inference) why it's not FATE 4E... it's a redesign "from the ground up."