I do not think you can simply mark one RTS as the best one ever....
Homeworld was for example perhaps the best single-player RTS, but its multiplayer was lacking, other games were just better multiplayer-wise, but not as immersive or innovative.
CoH, DoW, Sins, C&C´s, Starcraft, Warcraft, AoE, Conquest FW, Earth 21x0, Sup Com. etc...are all great games as well.
I can recommend to anyone one old not so famous game though. It is called Star Command Revolution, it was competition to StarCraft on its day and while it never became as popular as StarCraft, i always liked it more. It´s special aspect are the battles, which required lot of smart micromanagement not based on the number of clicks per second ala C&C and using some special ability at right time, but it was more CoH-like. That means it was not only about bringing the right "counter" into to battle but you had to take range of fire, direction of attack and other things into consideration.
For example you had to destroy enemy starbase hidden behind the asteroid belt, which you could reach only with the fighters from your aircraft carriers. The base had the enourmous range of fire, so you had to move the carriers to fighter launching distance protected with your Point Laser Cannons, which shot most of the base´s projectiles down, then launch the fighters and retreat the carriers to safe distance to repair them...
Or you could build the missile turrets which you could move only by using unit called switcher...so you moved the turrets infront of your fleet and ripped incoming enemy ships to shreds....and then moved your turret-line again via switcher deeper inside enemy territory.
I think this is pretty similar to CoH´s deploying of machine guns or mortar groups, supression fire and other stuff, which makes the CoH so different and interesting...and fun. I wish someone would remake this game instead of StarCraft 2, which when it comes to using of units and micro looks to me exactly the same as 10 years ago.