Age of Empires 2 has always seemed to me to be about the best game in the world... I prefer it over C&C for a few different reasons. AOE is much more complex, with more units, more buildings, better chances to expand your base (always hated 'sandbagging' for second bases in C&C), more resources, and I think the engine is built better. (Espiecially since it was used in Star Wars: Galactic Battlegrounds
)
Of course the two games are difficult to compare since they are so vastly different... different by about a millemium.
AOE in my opinion is the number one greatest RTS of all time, C&C would probably be second. It depends on what you feel like playing i guess... If your looking for a quick distraction, fast action, and deaths that look like melting tomatos then I would go with C&C. If your looking more for a "lets build a massive empire and end them all in one fell swoop" I would definatly go with AOE.
in my expericance AOE games last about 3-4 hours (depending on a lot of factors) where C&C almost never last more than 1.
@Underlord: I got ur CSS joke before I read it was from CSS. Made me laugh pretty well :-P
Bet C&C half
Bet AOE all