Stones, Beatles, Tom Petty, Bob Dylan... it's hard to choose a best of anything. Much like music, miles have a very "different strokes for different folks" approach. The answer is that there is no end all be all "best" way to earn miles, rather different airline frequent flyer programs that have better values for your needs than others. Here are some of the best separated by need...
LONG FLIGHTS IN ECONOMY
The magic potion for using miles in economy is to mix the lowest amount of miles, with the least taxes possible. Book it! For most long flights in economy, namely, those that cross an ocean, you'll be looking at a standard 30-40,000 miles each way through many of the most common mileage programs like Delta, American, United, British Airways, Emirates, Etihad, JAL. Programs like Air France Flying Blue and Lufthansa Miles & More however, offer promotional opportunities each and every month allowing you to cut that number in a quarter or a half, on certain routes. Obviously that also means they are probably the best for long haul economy. 25,000 miles to cross an ocean works well with me!
Other Considerations: Delta, United, American, Virgin Atlantic.
Short Flights In Economy
This is one people have a hard time wrapping their head around, but even if you've never flown British Airways, and may never ever fly British Airways, they are simply the best miles to use for short flights anywhere in the world. The reason behind this is that you can use their miles, as little as 4,500 one way or 9,000 round trip, on partners in the US, Asia, Europe, South America and Africa; such as American Airlines, Japan Airlines, Cathay Pacific, Iberia, FInnair, Qantas and more. If British Airways miles aren't in your cards ANA, LAN and Southwest offer similarly low, lower than everyone else amounts of miles for shorter distance travel which can be especially useful in Asia and South America.
Other Considerations: Southwest, ANA, LAN.
Long Flights In Business Or First
Ah yes, there we are. The dream flights that miles make possible. If you're planning on using your miles for a bed and some fine dining on a plane, there are two main programs offering the best value for the world's longer flights: American and Alaskan. Again, just because you're earning miles on either airline, doesn't mean you have to fly them. You can use American miles to Asia, Europe, South America, Middle East, Africa, Australia or the United States as low as 50,000 miles each way in business class and 62,500 in First, on five star carriers like Cathay Pacific, Qatar Airways and Japan Airlines. Similarly, Alaska offer some great values as low as 45,000 miles for business class to Asia from Europe, or 55,000 miles for business class from the US to Australia. That's a lot of flying! If Emirates First Class is your dream, Alaska miles are your best chance at 100,000 miles each way. Finally, much like with their economy offerings, Flying Blue, the program of Air France and KLM offers the occasional 50% less miles for business class, which if you have points with American Express or Citi can be a great way to fly flat for as low as 62,500 round trip! Of course Singapore's Suites through the KrisFlyer program never hurt either at as low as 57,375 miles one way...
Other Considerations: Aeroplan, Singapore, Delta, United, ANA.
This is not the end all be all guide to planning the perfect trip. It is however a great start in pointing you towards the programs you should look into for your travel needs. I personally diversify my miles so that I have a nice chunk of British Airways miles, for any short flights in economy, some Singapore or similar miles for fancy flights up front and a steady stack of free agent credit card points, ready to go to the airline which fits my needs as they come. Happy travels.
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