The arguments on what shelter to take on the CDT are very similar to those I consider for every trek. I have a great ultralight tent, the Zpacks Altaplex. It's only 18 ounces and provides bug, wind, and rain protection. The only thing I don't like about it is that it takes up a lot of volume (relatively speaking), and uses most of the space in the pack's front pocket when it's wet. It also requires a short, 3 oz extension to my trekking pole for setup (it requires a 58" tall pole).
As my alternative I have two cuben flat tarps: a Zpacks 8.5' x 10' at 7.75 oz and an HMG 8.5' x 8.5' at 11 oz. The Zpacks drawback is that it doesn't have as many edge tie downs as the HMG. On the other hand, it has 'enough,' and it provides better rain coverage for the head and foot of my sleeping bag. To handle wet ground and condensation, plus bugs, I have to also take a bivy. My favorite is an MLD Superlight with an all-net hood at 5.3 oz. So I could do a tarp/bivy combo and have to carry only 11 oz instead of the Altaplex 18.
I really love the openness of the tarp. But to offset it, the bivy is a bit confining. You cannot spread your legs out when you feel like it. And you have to be careful rolling over. Though, the quilt alone has those constraints when it's cold out. And obviously, your bug protection does not support sitting up.
The other drawback of the bivy is that you cannot spread out your other pack belongings inside the dry tent. I carry an extra cuben cloth as a ground cloth for those items. That's another 1.5 to 3 oz, depending on which size I take.
I have to say, my clear emotional preference is to take the tarp/bivy. When I used the smaller tarp, I spent a couple of nights holding up the bathtub edges of the bivy to stop rain splatter from getting on my quilt (the bivy top is only water resistant). I haven't had that problem with the larger tarp.
My rational aspect says to take the tent to better handle bad weather and bugs.
So about two out of every three days I plan to take the tarp/bivy, and the third day I plan to take the tent.
My guess is I will end up taking the tarp/bivy combo.