If I had to guess at the reason for the delay in localization, I'd point at NoA/NoE. In Japan, Nintendo published the first title, but Level 5 handled it afterward. If you look at Layton's manual and the extras section, you see hints that the sequel was always supposed to head here.
I'm guessing Level 5 was asking NoA if they'd handle it, and they kept saying they would, and then nothing would be done. That probably continued for a while.
Now Level 5 has every reason to do it themselves - the sales of the thing are incredible.
This is all just a guess though.