GTI has a larger hatch opening to accept larger items. The GLI has a longer "floor" with the rear seats folded down, but the trunk opening will limit what you can actually load.
The GLI has two inches longer wheelbase, which means more ride comfort and more rear legroom, if that's important to you.
The GLI is 186 lbs heavier than a GTI. That affects acceleration, but also may add to comfort/stability.
The GTI has 145 lbs of extra carrying capacity, probably tied to the lighter curb weight. The details may differ slightly on the door jamb sticker, but VW's website states that the GLI's payload capacity is 893 lbs. The meat of four passengers adds up fast, especially if they're linebackers.
Then add luggage and you can reach 893 lbs quickly.
The GLI has a lower drag coefficient, which should return better fuel economy.
There's more, I'm sure. But those are the obvious ones to me. I had driven Jettas exclusively for over 18 years, but prefer the Mk7 GTI styling over the Mk7 GLI. However, I must confess that the GLI wasn't an option when I was shopping. Had it been, I may have gone that direction... maybe. Now that I'm in a GTI, I don't think I could ever go back. It's far too versatile to give up!