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Both will last as long as the way you use themallows. If you go around grabbing gears hard in a T56 you will bend up shift forks and wreck synchros like it is the thing to do(*cough RON cough*), if you regularly hold a 4L60E against the convertor and practice launches you will heat up the fluid and eat bands or just shatter the sunshell.
Both can be built to handle a substantial amount of power, the manual is usually much much cheaper to rebuild and repair though.
Also, take you daily driving into consideration. If you do a lot of inner city or traffic commuting, having a 6spd can get really old really fast. By the same token if you have the joy of a country road or more suburban commute, the manual can be a lot more fun for a "spirited" drive on a nice day.
Like Torque said, the rear is really the first weak link in the drive train. If you get into going to the track regularly, it has a better chance of lasting a while behind the auto.
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