However, you forgot to mention Age of Mythology! That game marked the start (or at least, sharp increase in) a decidedly modern RTS trend...
The use of player based special abilities!
That is, abilities that are activated outside of units and buildings. In Age of Mythology, they were called God Powers. They would show up, more or less in comparable form, in Command and Conquer: Generals, Command and Conquer 3, Company of Heroes, Rise of Legends, Battle for Middle Earth 1 and 2, and League of Legends. They're probably in even more games than that!
I think they represent a big difference between old school RTS's and the new breed.