Having both a manual car (finally!) and an automatic car in the driveway right now, here are my thoughts.
Glad to have purchased one of the few remaining cars where the MT version eats the AT versions alive for fuel economy. The Eco MT is 28 city/42 highway, while the Eco AT is 28/39. All the other Cruzes are rated 26/38, except the LS which is 25/35. The Cruze Eco's MT is geared such that its final drive ratio is LOWER than the AT, and the final few gears are lower than the same gears in the AT. The real-world fuel economy figures represent that. Many MT Ecos are averaging right around 40 mpg, including mine. Most other Cruzes are averaging right around 29-30 mpg. Maybe that's a selection bias due to how most of the Ecos are driven by people who want a fuel-efficient highway cruiser, while the other Cruzes are driven wildly differently.
I'm spinning 1800 RPM at 60 mph in a 1.4 liter 4 cylinder. There's limited power to gain speed, and I'm okay with that. It's sipping fuel, as it's supposed to. If more power is needed, 3rd is quite usable at highway speeds.
Our Fit with its 5-speed AT spins 2000 RPM at 60 mph. The AT loves to shift at the slightest hill, though. So it unlocks the TCC and wildly revs when it could have gutted it out with the TCC locked. That's just how it's programmed, I guess so the car feels like it has tons of power instead of grumbling/groaning its way uphill. It can be over-ridden, but it takes careful throttle application to get it to stay locked up in 5th when going uphill.
As one can guess, the MT Cruze gets better fuel economy than the AT Fit, despite the Fit's 300 lb lighter weight, smaller wheels, less HP/TQ, and overall smaller exterior dimensions. The transmission certainly isn't the only factor in that discrepancy. The Cruze's driver drives for efficiency, while the Fit's driver is a typical "mash and go" AT driver.
Also, in winter an AT needs time to warm up before locking the TCC. No worries about warming up the ATF enough to not damage the TCC locking up with a manual transmission. The Fit will cover 1-2 miles wildly revving a cold engine to warm up the transmission. My old Buick did the same thing. A MT car won't do that, only idling the engine a little faster to warm up quickly.
My answer to the original question is: It depends on the season, on the car, and on the road conditions. In summer with both cars warmed up, the AT car might be slightly more efficient. In winter with cold transmissions needing to warm up, the MT car will be more efficient.