Manuals are a lot more efficient. The problem with Fit manuals (or most recent manuals, really) is the gearing. In the automatic, top gear cruises at something like 2300rpm @ 65mph. In the manual it's more like 3100rpm @ 65mph, a whopping 33% faster. 4th gear in the automatic is very similar to the manual's 5th gear, so basically it's like the manual is missing a gear.
I can speculate as to why Honda did this: In Japan and Europe where Honda has no issue selling manuals and gas is more expensive, the final drive ratio is taller, RPM lower in all of the gears. Honda likely was trying to attract more buyers by making the car "feel" more powerful by keeping the engine at higher revs, at the expense of economy. Plus, you have to shift more frequently if your gears are taller. With the ratios in the Fit manual as they are, you can basically drop it in 5th at 20mph and never change gears, and who's actually going to miss that highway 3-6mpg anyway? :/
That said, my girlfriend averages 44-48mpg in her 2007 Fit manual, way higher than the combined 30mpg rating. She doesn't do anything special, she just doesn't drive it like a racecar. I expect manuals still have the potential to deliver better economy, but depend more on the driver's patterns.
