I personally try not to rip either system as a whole, as I think there are good and bad examples of both. The Civilization series is a good example of well executed turn based combat, frankly since I don't think the game would be easily playable in real time, considering its scale. Sins of a Solar Empire made a concerted effort to make a real time empire building game, and while it is fun, I don't feel that it has nearly the depth of any good game of Civilization or Alpha Centauri. As for Final Fantasy X, I think the system works better earlier in the game when your characters are weaker, and you have to plan how to beat stronger enemies, especially bosses. However, later in the game, when your characters can instakill anything in a single hit, all the strategy washes out and it becomes a bit of an annoyance, unless this instakill attack is extremely flashy or otherwise awesome (like weirdal suggests).
And as stated earlier, there are plenty of bad real time combat games too. Take Gundam Seed: Never Ending Tomorrow, for instance. You really have to work at it to screw up the controls on a console giant robot simulator, but they certainly succeeded with that one (particularly after the success of similar titles such as Federation vs. Zeon or the Armored Core series). Also, Haze for the PS3. I rented that recently and was so disgusted with the awkward controls, bad graphics, and pathetic attempt at a story line that I returned it immediately and played four hours of CoD4 to purge myself of the memory (I really hope Yahtzee rips that game a new one).
I guess what I'm saying is that it depends on the game and the gamer. Some games just have turn based or real time combat as a signature. I think even Yahtzee would cry foul if the next Civilization was real-time, much like he probably would if they made the next God of War turn based. If the game executes it well, turn based combat is just as good as real time combat. Either can be executed poorly, and I think that a poorly executed turn based game gets more rap since you're stuck for more turns staring at its shittiness, rather than having the distraction of rapidly killing shit in a poorly executed real time game.