It will differ greatly with different vehicles re the # of speeds. Many 3 speed automatics are just that and lock up for what feels like a 4th AKA "overdrive" and that same car might be sold with a 5 speed std.
The actual MPG you get will also depend mostly on you. Many times a std trans is less expensive and the car priced accordingly. If a first car for you or if you plan lots of stop and go as your routine I think you'll fare better with the automatic and either way it's a personal choice.
Some cars won't be available in standard trans at all,
T
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Tom Greenleaf - MetroWest, Boston