Based on the bike in the pic you posted in the your other recent post, it looks like your seat is set way too low (kind of hard to tell from the pic). When you ride your bike, does each leg nearly extend all of the way when your foot is at the bottom of the pedal stroke? Your leg should not lock out straight, but it should have a slight bend at the knee. You shouldn't feel like you are overextending your leg when you pedal, either. It does feel wierd to some people to ride like this at first because they are not used to a proper riding position.
Other than this, the only other thing contributing to the rough ride of your current bike could be that you are riding an aluminum bike, while your friend could be riding a heavy steel bike. Your aluminum bike could give you a stiffer, and therefore "bumpier" or "harsher" ride than your friends heavy steel bike (most dept. store bikes).
Were you riding on the trails or on the road? His semi-slicks or slicks could make a big difference on the road in terms of comfort and harshness of the ride.
You seemed concerned about owning a GT because of their buy-out. GT is still a reputable brand that (at least around here) isn't being sold in the dept. stores. The way I understood it, Pacific bought out Schwinn and GT. I thought that Schwinn would turn into the dept. store bike line, while GT would remain in LBS's for the most part. Either way, just because a brand is now sold in dept. stores, it doesn't mean that the bikes made previously aren't of good quality. I ride a Schwinn from before they were bought out, and it has held up great. Other than the occasional glances at races (everyone seems to think that it must be from a dept. store because it's a Schwinn), the name on the bike doesn't bother me. Ride your bike into the ground, and then look at other brands that interest you.
-Moab