Didja get out the measuring tape and set up both bikes identically? If your contact points are different, it can make the bikes feel different to ride. I also prefer to use the same tires and tubes as that seems to make a difference to me. Of course, even if you do these things, it would not be surprising that two different bikes of varying sizes feel too different. But it's worth trying setting them up the same if you haven't, imho. Cheaper than the hit you'd take selling the one bike and buying another.

Edited to add: Same "size" doesn't necessarily mean much even across different models from the same company. You'll have to look at the geometry chart to compare. I don't remember the link, but there is a good webpage out there with a downloadable Excel worksheet where you enter all the measurements of a frame and can compare the fit. Even different handlebars with different drop and reach can affect how one bike feels versus another.