Quarter inch is the defacto standard, is stronger and gives a little bit more "oops" tolerance as a first time builder. I am leaning toward 1/4. Anything else I should consider?

Paul:
I think that 'defacto standard' is moving toward 3/16, certainly under 1/4" by a bit, but I may be wrong.
Most builders seem to err on the 'just a bit more' side, and thicker strips are a LOT harder to bend and (especially) twist. A 1/4" strip is about twice as stiff as a 3/16 one (stiffness is proportional to the cube of thickness, IIRC).

My local supplier has 16' cedar, but I am leaning against it for two reasons: 1) 16' strips mean I need over 32' of space and infeed/outfeed support.

You can rip strips in the driveway. I fed long boards in through a window once. there is always a way!
You definitely need outfeed table support to rip 8 foot boards safely. I won't rip any board much longer than the saw table without outfeed support. You also need good feather boards - see Et's (Etienne Muller) advice on strip ripping, which is excellent.

When stripping with shorter strips I assume I would want to make sure to vary the location of the joints. I.e. not have all the joints line up on the same form -- correct?

Absolutely. Staggering joints may not make a great deal of difference to the strength, but it looks better, and more importantly, makes it easier to keep the surface fair- the adjacent strips help to align the sides of the joint.

Staple vs Less: I intend on building the hull stapled and will see how it goes before deciding on the deck.

Good idea. As I've repeated many times here (after a very long afternoon pulling broken staples) do some experiments with your staples, gun settings, strips, and form material before getting started. Modern staples broke for me on my last builds.

Skeg: The Petrel Play video series includes a skeg. As little more than a novice paddler, I don't have the experience to weigh the pros/cons, but lean against adding the complexity unless there are strong reasons to add one.

If a skeg is suggested in the plans, include it. As already mentioned, it is much easier to add it when building than to retrofit. If you don't like when paddling, you can always tape over the skeg box opening and leave it 'up'.
A friend recently did a beautiful job on a S&G boat kit, omitting the 'optional' skeg. She's an expert paddler, but after some paddling in rough conditions, she wishes she'd put the skeg in...