The amount of CC and mobility in League of Legends would make CTF a nightmare to balance.
Scenario 1 - No restrictions
Twisted Fate gets the flag, uses Destiny, Team A wins. Tons of champions can easily escape with dashes, blinks, or teleports that make it impossible to catch them.
Scenario 2 - No movement abilities while carrying the flag
You gets the flag, but cannot use any of your abilities while holding it.
Skarner shows up, pulls you back into his team who try to murder you while your allies 4v5 the enemy.
The majority of champions here are made for magical guerrilla warfare. Not retrieval missions.
While I would LOVE to play Capture-the-Flag on a League of Legends setting, it's not something I can see being balanced.
And before anyone suggests "What if we have assigned roles? Like: Only the chasers can hurt chasers and Flag-bearers can... etc etc" - This would cause a whole new mess of balance problems based on how well certain champions match up against others and would be completely inconsistent the current two modes where everyone has fair shot with at least damaging and fighting one another.
TL;DR - Nice thought, but would be impossible to balance