Sounds like some minor fit and component issues.
I have two road bikes and try to set them up as closely as possible, but the frames are slightly different sizes and designs, so the best I can do is approximate the fit. I *feel* slightly slower on the 25 lb steel bike, but in actual practice my average speed over 20-50 miles is pretty much the same as the -20 lb carbon fiber bike. The main difference is on climbs where the carbon bike feels quicker even when it isn't. It mostly means I'm conserving energy overall. I tend to average 16.6 mph over 20-50 miles on the steel bike, and 17 mph on the carbon bike. There's some consistent difference, but not much.
I thought a set of semi-aero wheels might offer significant improvement, but it hasn't. Original both bikes had very similar old school low profile rims, 32 round spokes each, same or similar Continental tires. Recently I tried the carbon bike with a Bontrager Race Lite Aero wheelset -- 30mm profile rims, 16 flat bladed aero spokes per wheel, less weight -- and *thought* they were faster. But in checking Strava segments over time, I can't demonstrate the wheels are any faster. They feel stiffer, as if energy transfer is more efficient. But that hasn't translated to significant differences in times and speeds over distance.
Where I *have* found significant differences is chasing marginal gains throughout the bike: chains and lubes (wax seems faster, but demands more attention); replacing the original rear derailleur pulley wheels with sealed bearing pulleys (Tacx, only around $15 a set for the black plastic Delrin wheels); chromed SunRace freewheels instead of the original Suntour and Shimano. These all reduced felt drivetrain resistance -- I can also feel it pedaling by hand with the bikes on a workstand or trainer.
I've swapped the steel bike from 52/42 chainrings to 50/39 or /38, depending on the wheelset and freewheel or cassette I'm using (usually 13-25 or 13-28, depending on the terrain). Keeping in the sweet spot helps my efficiency and overall speed.
The other bike has Biopace 52/42, and even after several months I'm still not quite persuaded. I had to change my pedaling style to make them work. But I'm still not feeling or seeing much advantage, and occasionally they feel a little sluggish, as if the oblong rings were introducing a bit more drivetrain friction or variation. Only way I'll know for sure is to replace them with chainrings and crank arms matching the other bike.
Speaking of which, does your wife's "new" bike have the same crank arm length? Minor variations matter to some folks. Other folks say they don't notice any difference between 170, 172.5 and 175. Some swear by 165 or shorter.
Saddle and position too. More little things that add up to measurable differences, especially over distance. My two road bikes have different saddles (130mm wide solid Selle Italia on the carbon bike, 140mm Bontrager Ajna with pressure relief cutout on the steel bike) and I can feel it when I'm riding. Takes awhile to adapt if I've been riding one for weeks without using the other.
Again, not huge differences between the two. But measurable via Strava analysis over time and many rides to reduce the effects of wind, weather, and how I feel subjectively.