Please not another TB vs RTwP flamewar here.
Both combat systems come with advantages and disadvantages and therefore each RPG designer should be free to choose what's the best for his/her game design.
Nobody would seriously compare the combat systems of Civlization and Age of Empires just because they are both somehow strategical.
Out of the context of a specific game design, there is no inferior or superior system.
We decided to go with a turn-based combat mainly because our game is based on 3.5e.