While I enjoy the playing both games I Believe StarCraft 2 is better because you are able to create worker units. Another great feature about StarCraft 2 is the pop. cap because it limits the number of units the play can have on the battlefield at one time forcing the player to think critically and tactically rather than spamming one unit type and throwing this unit at the enemy until victory is achieved.
(Before I make any further points I will allow my opponent to refute my claims and present their own claims)
I also enjoyed both games but first of all. Red Alert 3 has better graphics(slightly). Unit balance is actually pretty good but there are still one-man army units that could wipe an entire squad. And this amphibious-mecha things are fun. The online coop-mode and the great video cut-scenes can convince. And you mentioned about pop.cop, I think more units can enable you to think more critically than limited ones. And I never remembered spamming one type of unit to achieve victory.