The manual transmissions are usually more reliable and need less attention to keep them going. They also make better use of the available power. Fuel economy will likely be very close between the two. For 1st-gen 4wd Tacomas with the 2.7L, the estimate is 18 mpg combined for both transmissions, but the manual trans has one extra mpg (20 vs 19) on the highway than the auto (fueleconomy.gov).
If you already have a capable 4wd, why not daily drive a car instead of a truck? For getting from place to place on the road, I much prefer a car. The comfort, maneuverability, and cost of operation are so much better. Front-wheel-drive compacts with manual transmissions are my personal favorites.