No question that the higher mix ethanol gasoline will cause mileage to drop......
What kind of mileage are you getting?
Another thing that will cause the mileage on 3rd gen runner to drop is a degraded front (ahead of the catalytic converter) O2 sensor..
Experience, and discussion with a trusted dealer service manager indicates you need to replace the front O2 sensor about every 75,000 miles. It's still working, but gradually operation is degraded by trace level contaminants in the gasoline.
Article:
http://www.4x4wire.com/toyota/4Runner/tech/O2_Sensor/
One other thing that will kill O2 sensors is the use of any sealants containing silicone anywhere near the engine intake or gaskets on the engine (gasket sealant outgassing vapors will be sucked into the intake via the PCV system).. Silicone free gasket sealant has been available for quite a few years due to this..
O2 sensors are tricky enough in their operation that it's a bit of a risk to replace with an aftermarket sensor. Some do not have the right probe length and won't work properly.. If you ever replace it, get it from a Toyota dealer.