I don't think there is a hill of beans difference and it is now even less. You can/have to pay for extra leg room. DO by all means check the total flying time if you have changes.
Price is already going out of sight, and pack light or it will be even more, as of August.

Midwest - unfortunately abram, the Signature Service flights are going away. They are putting those Signature Service seats only in the front 3 rows and you have to pay a little extra for them now. But wasn't it a lovely way to fly? Even without the Signature Service, I still prefer Midwest, but then they are my "hometown airline."

I live in New York City, so I am fortunate to have many options from 3 major airports.

Non-stop is a priority. I don't connect. Ever. (Well, on occasion, when the destination is St. Bart's or Anguilla and I don't have a choice.)

JetBlue is my favorite carrier, but I prefer LGA over JFK, so I'll fly out of LGA all things being equal.

I choose based on:

price
dates (willing to switch if travel dates not set in stone)
non-stops

I've chosen JetBlue over the legacy airlines many times. Just personal preference. Of course, then I lose the ff miles, and that makes me kinda sad, as I want it all.

Virgin America from NYC to LA and SFO because of the service, comfortable seats and leg room. They just started flying last fall. It blows any of the other domestic airlines.
Continental for flying down south from NYC. It's an easy option as their main hub is Newark airport.
Internationally, Continental to Rome, Athens and Paris as they have great transatlantic service and comfortable seats with great leg room.
In the future, I will fly Quantas,Air NZ or Singapore to OZ,NZ, Thailand and Japan.

Lufthansa.

I've flown with them twice in the last year. I've found them to be very friendly and efficient [cliche but true].

Lufthansa, due to anything you can think of....

Most of the time, I shop by price. Yes, it is a balance between price and schedule... but it is not an even split. I'd say 70% of it is price and 30% is schedule.

The only airline I really try to avoid is US Airways. This stems from a dispute I had with them over unused funds. Basically, on the phone, I was told that if I needed to cancel my flight I could apply the funds to another trip within one year. I booked the flight and then, due to unforseen circumstances, had to cancel. It was $139 roundtrip. Later, when I went to apply those funds, US Airways insisted on charging a $150 fee to apply them. This was not only overlooked in my phone conversation but it also made no sense. They credit me $139 and then charge $150... so I end up paying $11 more! They continually insisted that they had no choice but to charge the $150 fee so I lost my $139 but they lost my business and my company's business.

So, my advice? Do not fly on US Airways. I have never had a significant problem with anyone else, however.

Jet Blue is my # choice but their times and airports are limited. I like their customer service, TV's on the back of every seat.

For time and price, my #1 choice is Southwest.

Midwest Airlines - whenever it will take me where I want to go. Just bought my tickets yesterday for San Francisco. Midwest is having a terrific sale right now.

When I picked out my seating there were more than 3 rows for the upgrade to Signature seating but $50 for an upgrade is not worth it to me. The number of rows for Signature Seating could depend upon the plane.

Will find out if I want Signature Seating after I sit for 3 or 4 hours in the "cheap seats". Not sure if they made Signature seating more roomy or made the regular seating smaller.