I just picked up a Superfly AL to replace my Cobia. The Superfly bars were much wider than the Cobia bars, 700mm vs 600mm. So I cut the Superfly bars to around 620mm. Even with the shorter bars, the Superfly steering feels quicker than the Cobia steering and I find myself overcorrecting more than I use to. It's a subtle feel and I did just start riding a new trail so I suppose I could blame the trail. But is there any reason why there would be this steering difference, such as geometry, stem selection, etc?

Shorter bars and shorter stems = quicker steering, IME.

Cutting 'em down probably made things a little perkier.

Other things that could make steering quicker are steeper HTA, other steering geometry differences and weight distribution farther back, as a result of STA, saddle setback, higher bars or shorter stem.

Not sure about the HTA, but I noticed the stem angle isn't as high on the Superfly. It's not marked, but looks like a 5 degree. The Cobia is a 10 degree. Both stems are the same length.

How long is your stem & what are the angles of the frame, both will have a effect of the steerering feel / speed.

For your handlebars, 700mm normal, if not on the narrow side for 2012, 620mm is like riding a bike from the mid 2000's, geometry and stem lengths have moved on since then.

Stems are both 90mm. The 600mm bars feel fine on my 2011 Cobia. I didn't think that much would be different on the 2012 Superfly. I'm not sure about frame angles.

Unfortunately Trek doesn't keep the Geo page up in their archive of the 2011 catalog.

You could always do what I do when trying to replicate bike setup. Put your camera on something (tripod is nice but box, chair, etc also work), try to align BBs with something on the wall or floor, take pics with both bikes then superimpose in PS, the GIMP, etc.
Then check fork settings so you have similar sag from bike to bike.

mongoose vs trek by Lester Of Puppets, on Flickr

Cool approach. I'll have to give it a shot and see what looks different.