We flew Jet Blue on the 2 X 2 planes. LOVED them!!! I took a DD and DH sat with one across the aisle...it was perfect. Much better than the 3 X 3.
The always board the back rows first and then they call the front section. So if you are in a hurry to board the plane, you would want to be near the back. There are usually two washrooms back there too. If you sit near the front, you usually board in the second group or sometimes third, depending on how they want to split it up. But you get off first!!! I think there is one washroom at the front of the plane too.
I always prefer to sit near the front. I like the option of getting off the plane faster. If your kids are young, you get preboarding anyways, so it doesn't matter where you sit, you get to board first. It's not necessary to pay extra for the extra space because I find the JB planes pretty roomy anyways, I would go for the first row of seats behind the premium seats.