I was expecting to get the same speed from both routers but the primary is around 3 times as fast as the extension.
Although it might be surprising, the extending AirPort Extreme should not be set up to "Extend a wireless network". That setting would only be correct if the extending AirPort were connecting to the main Extreme using a wireless connection......not Ethernet.
So, as forum expert Tesserax mentions, the second AirPort Extreme should be set up to "Create a wireless network" that uses the exact same name, security and password as the "main" AirPort Extreme. Additionally, the second AirPort needs to be set up in Bridge Mode, which Apple calls "Off (Bridge Mode)".
Even if the second AirPort is set up correctly, there are no guarantees that a Mac, iPhone / iPad etc, will automatically "switch" to pick up the signal from the closest AirPort when the device changes locations. Check to make sure that the device is connected to the closest AirPort when you want to perform any speed checks, etc.