Another big topic is the places to which you travel. Going to Europe is different from going to San Francisco, which is different from Casper Wyoming. Boston is served by plenty of airlines, but you'll want to focus on one that has good connections to where you ordinarily travel.
Travel comfort matters a great deal, also. There are differences in award charts between airlines, but I don't think they're as big as the hours in the air. I wouldn't want to make weekly connections on small regional jets just to get 20% cheaper redemptions.
Availability also matters for hotels. For instance, the Starwood program is well liked, but it doesn't have much coverage in smaller cities and towns. I also think Starwood and Hyatt are a little pricier overall. Hilton and Marriott have greater US availability, but some places with lower quality.
I don't travel much now, just for conferences and holidays, so I look at memberships from a budget perspective. Up until this year, I only had travel within the States, so I went through Southwest. Rapid Rewards can be very efficient, but only if you want to go where Southwest goes. Now, I have international conferences to go to and Southwest isn't as helpful.
Other people here know a lot more about the programs, so providing the "travel-to" locations would help as well.