What are the advantages of having a USB rechargeable flashlight vs. removing the batteries to charge them in a battery charger?
Fenix rechargeable flashlights are certainly more convenient simply because you can plug the flashlight in and charge the battery without removing the battery. One disadvantage is that if the battery's voltage is extremely low (deep-discharged), you won't be able to charge it using the USB connection and will need a battery charger to "revive" the battery.
As for battery chargers, an advantage is that you can swap batteries out and continue to use your flashlight while you charge one of the batteries, assuming you have a spare battery. One disadvantage is that by continually unscrewing the tail cap or headpiece to remove the battery, the threads can wear out a bit faster.
Learn what to look for when purchasing a rechargeable flashlight.