The TJ D44 will have larger axleshafts than the D35, and won't have the narrow neck the D35 shafts have where they are prone to snap.
The old XJ and MJ D44's are a lot stronger than TJ D44's, having thicker axletubes for more strength.
Stock D35 axle shafts are 1.18" and 27 spline. Super 35 shafts are 1.31" and 30 spline, an increase in strength of 35% and the same size shaft as most D44's.
Many will argue that the super35 is merely polishing a turd, putting money into an axle and still having a turd axle. If you don't push the jeep hard and the stronger shafts will work for you, I say go for it. If you push the skinny pedal and don't want to fix and put money into something twice, install a real D44 or the Ford 8.8 rear.