I have a Trek 400 Elance- it's a beautiful bike, I think it's the prettiest bike I own. For whatever reason, riding it was a neutral experience. I didn't dislike it, but I didn't like it. I changed wheels (actually went from 700c x32 to 27 x 1 1/8) and I found I really liked the ride much better. Whether it was the better hubs, a larger wheel, more or less air volume, different freewheel... I don't know. It was a pronounced difference in the way the bike rode.
He is right. I had the same bike, a 751 Elance 400, and with a great set of hand-built wheels, it rivaled anything I had.
Weight makes very little difference, about 36 seconds for 5 lbs over a 71-minute ride (per Cervelo's tests).
So, if you rule out weight (which I generally do), you come down to, IMO, these factors, in order:
1-geometry/riding position - the same "fit" on different geometry can still make muscle groups work differently.
2-wheelset-a properly trued and tensioned set of wheels can make a bike ride "like new."
3-tires - some just seem to suck the power; I don't know why. Easily tested with high PSI, though.
There's also the "package" effect. Just like some bikes come together like a cloud with wheels, some come together like a stubborn mule.