Well I will get beat to death, but here goes.
I have a 2001 sport and an 03 rubicon, so I have both axles.
Your sport and rubicon have the same axle tubes, or at least they did when you still had the 35 under the sport. You now have larger diameter, thinner, slightly stronger tubes on your 8.8 than on the 44/35.
My 01 had a hammered 35. I'm sorry but the axle was junk. Did not want another tooth pick, I shoped for a 44, couldn't find one. Studied the 8.8 and became impressed. It is stronger by quite a bit. The big one for me was also the cost, it was $50. For that cost it has factory installed 4.11's and disc brakes. Yes, it is an inch narrower and the opinion shaft is offset. Neither has cause me problems.
"Junk" can mean different things. The Dana 35 was never shipped from the factory with any larger than a 30" tire mounted to it. That is the max it was designed for. It very rarely fails in stock form on any of the stock tire sizes. If it failed regularly, I think "junk" would be a fair way to put it. Since it rarely fails until either a locker, larger tires, or both are installed, I don't think "junk" is fair.
8.8 has a slightly larger ring gear than Dana 44, and it has 1 more spline (31 vs 30) compared to the Dana 44. They are virtually the same strength.
Things like finding them for $50-250 are the ONLY reasons folks choose an 8.8 over anything else.
Most aren't excited about 4.10s unless they have a stock tire 4.0 manual or a 33" equipped 3 speed auto. The stock tire 4.0 manual doesn't need stronger than the Dana 35, so he's probably not looking for 8.8s, 4.10 or not. Anybody else will be undergeared with 4.10s, so it's not such a win. Disc brakes are nice.
The inch narrower can be a problem, it depends. I'm not sure what an opinion shaft is, but yes the pinion shaft is offset. Your diff hangs down a bit lower than either of the other two axles, so that is a lose. May not matter for your uses.
Granted, had it I been able to find a 44 I would have went this way probably. But not at the $1000 plus.
I was not thrilled with the super 35 stuff. The axle is still a tooth pick.
Why would you go with a 44 if you think the 35 is a tooth pick? As stated, the tubes are the same. If you think the 35 is a toothpick, then you think the 44's are also toothpicks.