Since the AI can't adjust sufficiently in different scenarios, it's best that you gradually start to move away from auto- commands as you get more experienced with the battle system. Manual control is important when controlling battle efficiency.
When you encounter a new enemy for the first time, the AI likes to alternate between physical and magical attacks to test out the enemy's resistances. While it may not interfere much with the speed in normal battles, it can waste a lot of time in the harder ones.
- Say an enemy is weak against Fire. An AI-controlled Ravager will auto-input something along the lines of Fire - Flamestrike - Fire - Flamestrike in order to take advantage of the weakness-induced bonus to Chaining, as well as the bonus for alternating abilities. However, it's much more important to place emphasis on speed (since the rank you get is based on speed alone) rather than these bonuses by using a single consecutive ability instead, like Fire - Fire - Fire - Fire or Flamestrike - Flamestrike - Flamestrike - Flamestrike. This will be a lot faster than alternating the way the AI does.
- In a focused Saboteur assault where you only need to inflict specific debuffs or when you need to inflict certain ones (like Poison), it's best to inflict them manually. The AI will apply debuffs in the same way that it would in a normal situation, and may inflict the one(s) you want last or not at all.
- Against a Launchable enemy that is resistant against physical attacks, the Auto-Battle queue will consist of Attack (to Launch the enemy) and then a string of Ruins (something like Attack - Ruin - Ruin - Ruin). If two allies attempt to Launch the enemy at the same time, the slower of two will leap up into the air and start to attack from there, slowing them down considerably in comparison to if they had just stayed on the ground. Since it only takes one ally to Launch an enemy, having two enemies in the air trying to do this is pointless and will slow you down. You can prevent this by letting the AI Launch the enemy (which it will do by default) and then let your manually-controlled character unleash a string of Ruins from the ground.
Outside of battle, you can raise your party in ways that will force the AI to do more of the specific things you want it to.
- Focus stat growth, either through the Crystarium, equipment, or infusion, towards Strength or Magic. This lowers the chance that the AI will alternate between two different damage types in battle because if Strength is considerably higher than Magic, or vice versa, the AI will go towards using attacks that utilize the stat with highest amount, therefore making your AI-controlled allies more efficient.
- Avoid the carryover of unnecessary abilities when infusing monsters. This will enable your monster to focus on its strengths. For example, there's little need for a monster with low Strength stats to inherit Ravager -strike abilities (which are Strength based).