Q: Which program should I join?
A: Choosing a program has more to do with your travel and spending patterns than it has to do with the strengths and weaknesses of any of the available programs. For the most part, the pressures of competition have forced programs to match each other's offerings. So the choice of the "best" program is a very personal one.
As a general rule, you should join the program in which you will be able to earn the most miles. Assuming you will earn the majority of your miles by flying, you will accumulate the most miles in the program featuring the airline(s) you use the most. Frequent travelers should ask themselves which airlines they fly routinely. And having answered that question, they will have also answered the "which program" question.
In practice, choosing an airline program is usually dictated by two factors: 1) your home airport, which is likely to be dominated by one or a few airlines, and 2) your usual travel destinations, which are likely to be served by a smaller subset of the airlines flying into your home airport.
On the other hand, if you are an infrequent traveler, you may expect to earn the majority of your miles through transactions that don't involve flying (such as using credit cards, staying in hotels, or making investments; see Earning Miles on the Ground). Then, you should compare the competing programs' partners and choose the program that offers the most opportunities to earn miles and awards for non-flight activities.
Between the two extremes, there is a middle ground for those who divide their mile earnings more or less equally between travel and non-travel. If you fall into this category, you will have to consider both of the options above: 1) how the various airline programs award you for your travel activity, and 2) how they award you for purchases and other non-flight activities. If, for example, American and Southwest were equally capable of meeting your air travel needs, the deciding factor would be their respective abilities to reward you for non-flight transactions. Since American has a significantly more robust array of partners, its AAdvantage program would be the likely choice.
These days, travelers also have to take into consideration the financial stability of the airline whose program they propose to join. If the airline that best suits your travel needs is bankrupt or close to filing for Chapter 11 protection, you might want to think twice before putting all of your mileage earnings in that program.