When recording direct with a USB cord, the room sound you'd expect to pick up using a microphone is absent. Whether or not this is an advantage is a matter of preference. In some applications, cutting out room sound is desirable. For example, when recording a tight, percussive guitar track. In other scenarios, a lush, room reverb adds depth and character to the tone.
Amplifiers, especially tube amps, add tone and character to the sound of your guitar. In bypassing the amplifier and recording direct to the interface, you eliminate all natural amp characteristics from the signal and replace those qualities with a rather harsh, digital sound. It's possible to replace some of the lost characteristics with post-production effects, but it's extremely difficult to authentically replicate the exact sound of a good quality guitar amplifier.
When using a microphone, you introduce a number of variables that are not present when using a USB cord. For example, the angle of the microphone, the distance of the mic from the speaker and the shape of the room all influence the clarity of the signal. When using a USB cord, you get a very consistent and reliable level of clarity. While the average clarity of a USB cord may be lower than that of a good quality condenser microphone, you can at least predict how the guitar will sound when recorded via a USB cord.
It takes time to set up and audition a microphone. Due to the variable factors, you need to tweak the position of the mic, the angle, the volume of the amp and the layout of the room. This isn't necessary when using a USB cord. It's a simple case of "plug and play."
Microphones pickup ambient noise, wind, rain, squeaky floor-boards, coughs and the rattle of a beaded necklace. Because the a USB cord connects direct to the output of the guitar, the only possible interference is that of sounds projected loudly and directly into the guitar pickups.
When recording with a microphone, what the microphone captures is final and absolute. While you can tweak it, equalize it, compress it and mix you can't remove any of the sounds. So if you decide you don't like the guitar tone, you need to rerecord. When using a USB, you can edit the effects, tone parameters and volumes after recording. You have the option to remove distortion, add reverb and even use amplifier modelling software to emulate the sound of a classic amp. While the tonal authenticity of using an amp and mic is greater, the options for tweaking when recording via USB are huge.