Generally I believe skids are preferred for aesthetic reasons more than functional. For most sci-fi themes, including Wing Commander, the craft seem to be able to levitate, further eliminating the problem of friction.
As for a possible advantage, they would be easier to secure to the deck of a starship to keep them from rolling about on their wheels (modern carriers chain aircraft down to the deck to keep them from rolling around). As to the claims that skids could land where wheels couldn't I'd have to disagree as, on the grand majority of craft I've seen in sci-fi, the foot print of the skids are not that much larger than you could achieve with wheels.
Wheels are easier to work with when you have disabled craft to deal with though as you can simply drag them to maintenance, though the landing bay is usually the maintenance bay as well on most sci-fi carriers. Though even that could be overcome by killing the gravity generators on the flight deck, then it would just sort of float, weightlessly and you could conceivably move it by hand at that point, it'd just be tough for you to get its momentum going.
Planetside is where you may have difficulty. In a sci-fi universe I roleplay in, the fighter my character pilots has wheels for landing and movement on the ground since it lacks dedicated lifting thrusters, and the lateral thrusters lack the power to counter gravity.
Those are just a few considerations. Though I do believe aesthetics play out more than any consideration for functionality in most cases.