Pros and cons
Pros:
1. Apple is encouraging people to use rechargeables.
2. Apple's charger is offering the right technology - low-self-discharge (LSD) batteries and a smart charger.
NOTE 1: Li-ion batteries do not come in AA - you can buy some in that form factor, but the voltage is too high and you can't use them in a device that requires AAs.
NOTE 2: For most purposes, a 2000 or 2100 mAh LSD battery is a better choice than a battery with, say, 2500-2800+ mAh, as the 2500+ cells will lose all of their charge in 4-6 weeks. While this is not a disadvantage in all cases - if you are a frequent photographer and always charge your batteries the night before, for example - it is a disadvantage if you are using the batteries in a low power situation. Such as in a mouse, keyboard, remote, etc.
3. Apple's solution is only slightly more expensive than other alternatives.
Cons:
1. Apple's solution is more expensive than other alternatives - for $30 on Amazon, you can buy 8 Eneloops and an Eneloop 4-battery smart charger.
2. A 4 battery charger is better (specifically, more convenient, useful, and flexible) than a 2 battery charger.