Looking for advice, input from the experienced boaters out there regarding skeg versus rudder and what conditions one might want one over the other, is it just a factor of boat length/maneuverability, or if it is purely a preference.

Both skegs and rudders are mainly used to counteract weather-cocking from the wind. You don't need a rudder to steer a kayak. If your kayak is steering into the wind, then put the skeg down. You may need to bring your skeg up a bit if your bow begins to blow away from the wind. Both skeg and rudder cables require special care.

Rudder can also be partially raised to "tune" the boat for the wind and boat speed and direction

I generally prefer a skeg as it doesn't wag the boat when in use (it allows for a more efficient pumping action on the foot braces - one exception to this is a toe controlled rudder system where the actual foot braces do not move).

Both, however, have disadvantages: skegs can jam; rudders can break (rarely)..

Had one break in a surf landing by a trip participant. Seen more than a few rudders come down on fingers and get in the way of rescues...though that can be avoided.

You don’t need a rudder to steer, true. But using your body for long sustained periods to counteract the environment or make course corrections does rob speed and endurance, opposed to setting a properly designed rudder that allows good foot support and lower body engagement. 

The downsides are that a rudder gets in the way more than a skeg. It sticks out the back when deployed, and it sticks up when stowed opposed to a streamlined slick stern. There’s also some arguments to the mechanical complexity to a rudder leading to failures but Skegs have problems too.

My opinion depends on your paddling preference 

- touring, speed, and fitness: rudder

- maneuvering, rock gardening, playing around, rescues: skeg

personally, I go for a skeg unless it’s a go fast boat like an Epic or a Tiderace Pace 18.

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Agree. Also paddling on one cheek (edging) for miles get old...

I had a skeg cable kink and spent 10 plus miles paddling as a one-arm bandit in the wind -- no fun.

I'd never use a rudder in the surf and carefully use a skeg in the surf. When we go our to play in the surf we duct tape the rudders to the deck

Skegs tend to be used on more "performance oriented" boats. Boats of this category tend to have features like a hard chine that respond well to leaning motions when turning. Also with a skeg, the footbraces are sturdier and better at keeping the paddler connected to the boat while bracing, rolling and surfing.

Rudders more common on "kayak camping" oriented boats, which tend to be beamier and longer in order to carry more beer, barbeque and folding chairs to the campsite. Leaning a boat to steer that has a case of beer between your legs doesn't work very well -- and rolling a boat carrying such cargo is both nearly impossible and likely to result in loss of beer.

Rudder is primarily used for steering. While the preferred method for steering a sea kayak would be proper edging and strokes, with tandems and very narrow hulls, that can be more of a challenge. The rudder becomes a useful tool in these cases. The rudder CAN be used to correct for weathercocking, but it's less effecting at anchoring the stern than a skeg.

The skeg is primarily used to counter weathercocking by allowing the paddler to lock the stern (or release it). It's a great tool but I also recommend learning to edge and use strokes to help control weathercocking so you're not dependent on it.

While there are alternatives, the most common rudder pedal setups do not provide firm foot support, which makes it harder to brace and roll. Not impossible, but it's not ideal.

Rudders also offer unparalleled opportunities to snag your towline on the stern of your boat. George Gronseth's shoulder sling towline system gets the line up high enough to (mostly) avoid this, but a line attached lower to a quick-release belt around your PFD will snag constantly. As a big fan of towing, I prefer as clean a stern as possible.

Imagine if this guy had had a rudder:

https://www.youtube.com/watch?v=eCC-oX-OsWg