We usually rent from Toyota rent and all their cars have been with automatic transmission.
ECT card can be useful if taking a minor exit that does not accept cash. We always take an ECT card as it is convenient for the price.
Our cars had 50,000 - 60,000 km on the meter, but that is perhaps we are older and foreigners. Once we got a brand new car, but you hardly notice the age of the car as they are in very good condition.
With Toyota you can reserve your model of choice and it might cost a few yen more. We wanted a Carolla Station and it was available at pick up.