Read the terms and conditions of each programme, but generally:

• Differences in the ability to rebook
• Differences in the ability to cancel
• Differences in the ability to no show
• Differences in award program incentives
• Higher earn rate for miles

But most of all, not having to deal with an agent and instead work with the airline directly when things go wrong.

I simply don't book with agents. They just take money and add no value other than convenience. I'm not so easily fooled.