As someone who has played a tank in nearly every mmo ever, I almost always do the same thing to start a dungeon. First pull is 3-5 mobs. When that's dead, I look at the over all DPS, I look at how the healing felt to me, and I look at the healers mana. If it's all good to me, then large pulls it is. If any one of them is bad, then it's pack by pack.

I leveled SAM in Stormblood so not sure just yet about how hard the mobs are hitting tanks for but I will still use the same method while leveling my PLD I just started working on. But in reality, unless you are pulling all trash from 1 boss to the next, the runs really don't take much longer either way. The large aoe pulls actually put a lot more stress on everyone to shave off at most 3-5 minutes