For all that JetBlue Airways could do with the eight slots pairs it has acquired at both Washington Reagan National Airport and New York LaGuardia Airport, the most intriguing—and perhaps most daunting for Delta Air Lines and US Airways—is starting a shuttle-like service among Boston, New York and Washington.

The effects on fares could be dramatic, but might not be too damaging to Delta and US Airways in the long run, an Aviation Week analysis of the markets using Oliver Wyman’s shows.

JetBlue is not yet saying what it will do with the slots, with the airline and U.S. Transportation Department (DOT) having confirmed only Dec. 1 that JetBlue was one of the successful bidders. The DOT says JetBlue will pay $40 million for the eight slot pairs at National and $32 million for eight at LaGuardia; Canadian low-cost carrier WestJet will pay $17.6 million for eight at LaGuardia.

“By nimbly seizing opportunities like this unique auction, we will be able to significantly expand our low-fare presence in the nation’s capital and our hometown of New York City,” says Scott Laurence, JetBlue’s VP-network planning and partnerships.

JetBlue has offered flights at LaGuardia since 2004 and currently provides nonstop service to three Florida destinations, Fort Lauderdale-Hollywood, Orlando and West Palm Beach, with up to 10 daily flights. At Reagan Washington National Airport, where JetBlue began operations in November 2010, the carrier operates up to nine daily flights to its “focus cities,” Boston, Fort Lauderdale-Hollywood and Orlando.

Laurence does not say what the carrier will do with the new slot pairs—those announcements will be made “in the coming months,” the airline says—but JetBlue does note that its entry into the Boston-Washington National market lowered industry fares on the route by about 30%: from $168 in the second quarter 2010 to $118 in second quarter 2011.

That statistic becomes more interesting, and potentially more troublesome for Delta and US Airways, if JetBlue opts to add National-LaGuardia and LaGuardia-Boston to the mix.

The National-LaGuardia route provided Delta with more than $49 million in revenue from the third quarter of 2010 through the second quarter of 2011, carrying more than 254,000 passengers at an average one-way fare of $194.49, the PlaneStats data and calculations show. US Airways reached nearly $58 million in revenue, carrying more than 288,000 passengers at a $199.85 one-way average fare.

For both carriers, their highest quarterly average fare was in the second quarter, exceeding $218 for Delta and $229 for US Airways.

For Boston-LaGuardia, Delta generated more than $71 million in revenue in the same time period, carrying more than 360,000 passengers paying an average one-way fare of $198.43. US Airways brought in nearly $64 million, transporting more than 313,000 passengers at an average one-way fare of $204.06.

Again, the average one-way fare was highest in the second quarter of this year, topping $224 for Delta and $229 for US Airways.

Taking 30% out of those fares—if JetBlue’s presence were to make the same difference it made for National-Boston—would seem like a significant hit.

But take a close look at those National-Boston market numbers. US Airways has seen a big drop in its one-way fare, from $192.23 in the third quarter of 2010 to $135.25 in the second quarter of 2011. But that may have stimulated the market: it carried nearly 60,000 more passengers in the second quarter of 2011 than the third quarter of 2010, so its total revenue for the second quarter actually was about $2 million higher.

Delta does not operate National-Boston as a shuttle route any more, but there still was a similar effect on the service it offers on the route. Its average one-way fare declined from $143.92 to $113.64, but it carried about 10,000 more passengers and raised about $550,000 more quarterly revenue.

That did not stop JetBlue from succeeding. In the second quarter of 2011 it carried more than 85,000 passengers—about half the number US Airways carried and about 2.5 times more than Delta—at an average fare of $100.59. For the year-long period, without having operated on the route in the third quarter of 2010—it carried more passengers than any carrier but US Airways.

One question, of course, will be whether there is room in the National-LaGuardia and Boston-LaGuardia markets for another carrier to operate profitably. But one possibility is that American, which unsuccessfully tried a shuttle service last decade with its America Eagle product, could pull out of the markets entirely as part of its bankruptcy restructuring and capacity cutting and place its code on JetBlue flights instead. American already is placing its code on JetBlue’s nonstop service between Boston and Washington Dulles International Airport.