Card-Reader Can Still be Faster

A camera might be designed to write 35 megabytes per second to the card and handle the “U1” standard, and reading back out is oddly capped at 20 Mbytes/s due to the USB chip used, which is only USB-2.

You can buy even faster cards, e.g. “U3”, and USB-3–based readers that can let you dump the card at 95 Mbytes/s.

This will probably always be true as the hardware cycles up. You will be able to find even faster cards that are compatible with the camera, and even faster readers to use when dumping them.

Camera's Reader Might be Hard to Beat

The Canon 1D X Mark II has gigabit ethernet for a transfer interface. The camera's CFast card is faster than any USB-3 card reader could produce.

Built-In Bridge is Not Nice

Although the OS has built-in knowledge of a standard file transfer protocol for cameras now, some cameras might not be quite compatible with that and demand their own special drivers and bloatware, even if you then ignore that and use standard file transfer tools.

The camera mounting might not be a full file system that appears for use with all file-based tools, but only works with the operating system GUI shell for dragging files. That makes it difficult to use a script to copy-and-verify, for example.

Camera's Utility Software Can be Good

The EOS utility might in fact be your preferred transfer method.

Bundled brand-specific software might take specific advantage of the camera's direct connection. 3rd party software is likely to use a file system mount as well as photo-transfer protocol, if copying the files is all it's doing.

Power—good

Some cameras might recharge on the USB, so you can charge and transfer at the same time. Or at least transfer and then turn off to charge without moving it. If it takes 2 hours to copy the files off, hopefully it will turn off by itself or switch to charge mode by itself unattended, so that's more of a potential benefit. (Please edit with real examples if you have one and use it that way)

Power-bad

The spent cards and battery get taken out of the camera, with the batteries going to the charger and the cards going to the computer. Leaving a battery in to use the camera as a card reader would be more hassle.

With it taking hours to transfer all the files from a large card, the use of battery power on the part of the "reader" might be a bad idea in general.