In part they are two distinctly different models. The hub and spoke legacy model dictates that much of the feed to the hub come from feeder cities. Feed needed for both domestic and international flights. Flying to low traffic airports (moreso in the past) allowed southwest to avoid traffic delays at the legacy hubs. Also, southwest's turn times (and non-major hub flights) provides for more pilot productivity and efficiency.
However, they are becoming more and more similar. Southwest just dramatically revamped its frequent flyer program to better match the legacy programs. It will drive more loyalty and now includes the ability to fly to Hawaii and internationally. Not identical to traditional programs, but more similar than ever before.
Speaking of operating more like legacy carriers, this is certainly not the greatest news for southwest:

Southwest on-time rate falls to less than 55% says data report
By Lewis Lazare Media/Marketing columnist Jan 6, 2011 6:17AM
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10-12-10 Southwest Airlines at Midway airport. photo by Jean Lachat/Sun-Times
Southwest Airlines’ on-time arrival performance took another huge hit in December, according to data released this week by Portland, Ore.-based Flightstats, a respected provided of airline performance data.

The grim news for the low-fare carrier came as the U.S. Department of Transportation asked Southwest Airlines to explain why the data independently collected by Flightstats has begun to diverge so markedly in recent months from the on-time statistics Southwest internally generates and provides each month to the DOT.

According to Flightstats, only 54.65 percent of Southwest planes arrived on time in December. “On time” is defined as arriving at the gate within 15 minutes of the scheduled time. In December Southwest was dead last in on-time arrival performance among the 42 largest domestic carriers Flightstats tracks each month, the first time in recent memory — perhaps ever — that Southwest has been at the very bottom of the list.

Even though bad weather was a major factor impacting on-time performance for many carriers in December, both United Airlines and American Airlines still got 82.61 percent and 80.47 percent of their flights respectively to the gate on time for the month, according to Flightstats.

Southwest spokeswoman Brandy King would not reveal the airline’s own internally generated on-time arrival data for December, but she did say it was “significantly” higher than the 54.65 percent Flightstats is reporting. There was also a significant discrepancy in the November numbers.

Southwest executives in recent months have repeatedly said they were at a loss to explain why the Flightstats data has suddenly begun to differ so markedly from the airline’s own statistics. But the carrier has conceded it is grappling with several big operational issues, including record load factors and a growing number of connecting passengers at airports such as Chicago’s Midway, where Southwest is by far the dominant airline.

Record load factors have made it tougher to deplane passengers and load outbound travelers in the 25 to 35 minutes Southwest typically allots for the process. And increasingly, outbound planes at airports such as Midway have been held for late-arriving connecting passengers. Getting connecting luggage to the right planes has been a struggle as well.

Southwest also recently announced new senior executives in both its operations and scheduling departments, two key areas directly involved in the airline’s on-time performance.

For the past several months, Flightstats has indicated it was eager to work with Southwest to figure out why its data has begun to differ so markedly from Southwest’s internal statistics. Flightstats did get a call from Southwest after the Department of Transportation said on Tuesday that it wanted an explanation. “Flightstats is pleased to be working with Southwest,” said spokeswoman Meara McLaughlin, adding “we only want to represent true, timely and accurate data about the airlines.”

Southwest Airlines On-Time Arrival Performance August through December 2010

Flightstats U.S. Department of Transportation

August 81.2% 82.3

September 78.50 86.3

October 65.48 77.9

November 66.56 not yet released

December 54.65 not yet released