Here's the biased opinion of a Pygmy Arctic Tern builder:

Plusses for Pygmy: beveled shear panels leads to fewer whacked fingers when paddling -- beveled deck holds its shape when mated to the deck, it goes together without forcing -- nicer flush hatches (though a bit more time consuming to build) -- raised bow and stern handle big waves better, reduce wash-over, look more like traditional Greenland kayak

Plusses for Chesapeake: smooth cambered deck -- scarf joints (the fiberglass-taped butt joints on my Pygmy came out cloudy, but could be avoided if you get a bubble roller as shown in Nick's book or just be very meticulous with your squeegee) -- one-piece cockpit coaming -- nicer deck rigging attachment than Pygmy's plastic pad-eyes

When I was just starting to look into building a kayak last fall, my gut feeling was that I liked the Chesapeake better. But then I made a checklist of features I liked, and found the Pygmy better suited me. Either way, though, you'll love your boat.

Hope this helps! Dean