Actually comparing the US web site with Jet Blue or Southwest is like comparing ATL with PIT. The airlines are in a completely different league. Neither SW nor JB have global services and neither has the route and fare complexity of US, especially JB. A fairer comparison might be US with UA, DL or CO. Not saying US would fair much better, except possibly with UA.
This is an important point. However, since US is trying to be a LCC (or says they are), they have to have a website with competitive functionality to WN and B6. Also to be a LCC, US needs to drive out a lot of their fares/rules complexity.
If we are simply talking about booking engines, WN, AS and FL have the best in my opinion because you can see all the available fares for each flight and then pick your fare. It gives you the opportunity to "buy up" to a less restricted fare, or in the case of FL, to biz class. I love how WN's website allows you to cancel and rebook, and then store your credits online, and it easily refunds taxes when you cancel a booking. Works beautifully. I think jetBlue is behind FL since FL has implemented the new functionality of NewSkies while B6 is still on OpenSkies. I don't see how Orbitz can be rated much better than US Airways, since they both use ITA for booking. Right now US is just having trouble getting everything working, but eventually I don't see how it will be any worse (or better) than what Orbitz has.
My rankings:
1. Southwest (ability to buy-up, ease of changes, credits & refunds. plus DING! is innovative)
2. Alaska (ability to buy-up, applies discount certificates easily)
3. Air Tran (ability to buy-up)
4. United (has troubles, but usually works for me. Ted has the "buy-up" functionality. Can see availability buckets. Allows me to buy tickets on US without having to deal with the US website)
4. Northwest (zone certs work very well, but nothing else distinguishing)
4. Continental (never had a problem)
4. AA (nothing distinguishing except they can be good about displaying other airlines fares)
4. B6 (works fine and is easy but nothing fancy)
4. YX (never had a problem and discount codes always work as they should)
5. US (this is kind of incomplete because it is still being worked on. Never tried a discount code. Matching functionality to Orbitz, but is easier for me to find a trip I want on US and then buy it from UA)