I first had CD in the car when Sony released the first in-dash player, the CDX-R7, way back in the mid 80s. So I've had a long history of CD players on the road.
I haven't used CDs in the car since 2012, when I bought a JVC in-dash with both a front-mounted and rear-mounted USB port. It has had a 64GB Sandisk Cruzer Fit in the front port for the past few years, but I originally had a miniature 60GB portable hard disk tucked into the dash.
In a newer car, I've installed a Pioneer 4200NEX head unit that also has two USB ports, plus an SD card slot. I ran a dual USB 3.0 extender to the center console--works perfectly. One port I use for the phone (mainly to use the head unit for navigation with Google Maps), but use a 256GB Sandisk Ultra Dual USB thumb drive loaded with FLAC (including hi-res up to 24-bit/192kHz) in the 2nd USB port, and also use a 128GB SD card. Capacity is 15,000 files/1,500 folders per device, so I can still load up quite a bit more once I get enough storage. I am considering an SSD for the USB port, actually, as that can hide in the center console and stay tucked out of the way. Loading files is a cinch since my collection is already ripped and stored on two different NAS boxes.
Pros to SD card/USB thumb drive: I no longer have to worry about burning copies to play in the car, nor do I have to worry about taking the originals in the car and risk having them damaged (I used to carry one or two CD wallets around with me all the time.) I also don't find myself forgetting to bring certain music titles with me--I have most of what I want to listen to with me in the car. No more skipping, no more CD drives going bad over time, or working poorly in cold weather. Also, there are no longer any CDs or CD wallets in plain view in the car--out of sight, out of mind. And the deck has a removable faceplace so, when I'm parking away from home I can remove it.
Cons: ummm...like, none?
I have Aux ports on the head units, but messing around with a portable player while driving is a really bad idea (especially with bad eyesight), so I scrapped that idea almost immediately. I also don't care to stream from a phone and burn through data, and I will not store music on a phone either--I would constantly be shuffling files on and off if that were the case.
And with leather seats, I cannot staple my Victrola 45 to the seat next to me anymore...
(Yes, I do actually own the 45-EY-3!)