With the 96-00 Civics, there is a VERY noticeable difference in acceleration, because the a/t actually drops the engine rpm too far when it shifts from 1 to 2. Also, when you need to pass on the highway, you can quickly pick your gear and step on it, if you have a 5spd, but with an auto (on this particular model), there is a brief lapse in power as the a/t tries to shift to a lower gear.
That said, an automatic would be better for a person with a bad left knee or leg, wrist/arm problems, or other medical issues which may limit joint movement or coordination. Or, for a person who places convenience and ease of operation over performance and economy. As for me, I'm glad I have a 5 speed.