It depends on if you know where your destinations are going to be, what your priorities are in terms of NYC airports, and what you think about the UA/US merger.

If you're flying mostly in the Eastern time zone, you have CO and US, depending on if you prefer EWR or LGA. I can't see flying American Eagle, or United via IAD, or DL via ATL when you can fly nonstop.

If you're flying primarily to the Central time zone, you have a lot of options. CO/NW works, as does a merged UA/US as well as AA, although American Eagle isn't as good as United Express in terms of small-city coverage. If the cities are right, then you also have Midwest Express and 2-2 seating.

If you're flying west of the Rockies, then you need to look at the transcon services out of EWR/JFK and see which one you like and which has the connections you'll need.