Naturally the 8.8 is a stronger axle, overall, when compared against the D35, even when in "Super" forms. The 8.8 was engineered to propel heavier vehicles, therefore, on average, the 8.8 would encounter more stress. The designers knew the loads it would endure and so they built the axle to hold up accordingly. This doesn't make it indestructible or the best solution for an "upgrade" though, it just makes it a RELATIVELY strong axle option.
An 8.8 swap as I see it:
Pro: heavier mass will work towards keeping the bottom side down
Con: heavier mass will require more engine effort to accelerate from a stop
Pro: larger components and pumpkin will distribute loads better
Con: larger pumkin will decrease ground clearance ... are the larger internals necessary for this application?
Pro: Disc brakes, overall stronger axle platform to start with
Con: Grinding and welding and associated fab work, yet offset center and narrower track, get any vibs?
Pro: Larger diameter tubes
Con: Thinner tube wall; lose tire grip and drop tube onto a rock, will it bend easier?
Pro: All signs are that it can hold up to moderate abuse
Con: All signs are that S35 axles can hold up to moderate abuse
To me it seems more like the trendy thing to do, rather than the practical thing. I for one love the disc brakes, but the narrower width and offset pumpkin turn me off regarding the 8.8 swap. For me to get a 4.10 axle around here, with low miles, it will cost 5-700 bucks. That is once I pay a core charge and trailer it home ...
Then all the other hardware I'd need to buy to swap the thing in, plus hoping I get the pinion angle just right (or whomever does the welding hopefully cares enough to do it right since it's not really their axle so they have little invested interest) ... Then after that is all said and done, it still has an offset pumpkin and narrower track (that would be easily noticeable for my eye).
All in all, I just don't see it as a necessary swap. Sure the D35 in stock form is known to break axles at the worst time, but I have seen nothing but positive feedback from folks that have built the 35 and wheeled with them.
If there is an anti-S35-annonymous group out there, then someone please direct me to them, because most that have done the upgrade and have given credible experience with their use are quite pleased.
Not everyone that owns a Jeep has 40" tires and is looking to crawl over the most abusive obstacles, so the need for maximum axle is not as common as the hype ... and if that is the case, you need a superior axle in all regards, then why would anyone humor the 8.8?