It's worth looking at what Tesla recommends for its (Li-Ion) batteries in the Model S. Range and overall battery life are a lot more important in a car than a phone.
The strong recommendation is (1) keep the state of charge between 20% and 80%; (2) NEVER run the batteries down to 0%; (3) only charge to 100% occasionally, when you want (in a Tesla) maximum range for a long journey; and (4) don't charge when the batteries are extremely cold (0C or less) - the Tesla will actually divert current to warming its batteries before beginning a full charge.
The Tesla supercharger is very careful about how it charges. It will charge slowly at first if the SoC is low, then increase to full charge rate and drop off again when the SoC reaches around 80%. So it might take 2 hours to get to 80%, and ANOTHER 2 hours for the remains 20%. I hope the Apple charging system is also smart.
Which leads to the question of whether an Apple charger is better than a cheaper but faster OEM charger. I believe that charging is managed by the iPhone or iPad, not by the charger, so that would indicate that OEM chargers are OK. However, the Apple charger is pretty smart about how it rectifies mains AC to DC current and in its design for safety, and these factors are worth extra cost over ultra-cheap alternatives.