Based on using the Pypes 2.5" side exit kit on my Dad's El Camino (fit great!), I bought the 3" kit for my Malibu.
I too was very frustrated with Pypes about not offering a side exit 3" x-pipe kit. They DO offer the side exit in cat back, but not for headers. So stupid. I emailed, called, and talked to several people and they just wouldn't do it. I even tried to by the 3" side exit tailpipes and they said they ONLY sell complete kits and wouldn't do it. Every time i have seen a car with the Hooker 3" side exit kit I wish I had ponies up the extra cash.
On top of all that, the 3" kit fits like crapola compared to the 2.5" kit. The issue is getting the pipes to tuck up into the driveshaft tunnel so they don't hang low. The X pipe is too wide to the rear so they hit the frickin floor boards. The rear of the X needs to be a tighter angle so the mid pipes could be closer together and the pipes would fit up into the driveshaft tunnel better. You can see in the pics how I shortened one midpipe, which drew it a little closer to the tunnel but no nearly enough. It also didn't leave enough room for the band clamp. I'd recommend the narrower band clamps with this kit.
I really wanted 3" even though I knew I didn't need it. It does sound really good though. In the end, I would either go with the 2.5" side exit or pony up and get the 3" Hooker kit if you want side exit. I cut mine off at a slash under the bumper.