To me, the Super 35 pros vs the pros of the 8.8 outweigh the cons of the 35. So, the Super 35 wins for me.
It makes your Dana 35 strong enough for 35's. You can either buy a kit with 30-spline 1541H shafts that includes an ARB or Detroit locker, or you can buy the shafts separately and buy a 30-spline Eaton E-locker.
The 8.8 is a great axle but it takes so much work to put into a TJ that it isn't worth it in my opinion. The 8.8 can be built strong enough for 37's. The front Dana 30 and 44 can not. So, what are you going to do if you want 37's? Well, you'll never find a stock width front axle that works so you'd have to get a new rear axle to match the width of a full width front axle anyways.
Both axles are capable of 35's so it leaves you with picking what you want.
The Super 35 will bolt in, it will remain a c-clip axle, you won't have to do any fabrication of any kind for it to work, and you have the gear ratios available from 3.07 to 5.13. You can still convert it to disc brakes later down the road if your heart desires, or you can leave it alone. The downside (if you can call it that) is that the ring and pinion are weaker than the 8.8...but this has proven time and time again to not be a problem so I would not worry about it at all.
The 8.8 does not bolt in, the housing is offset, the tubes are larger yet still the same strength as the Dana 35 (35 tubes are thicker), the stock shafts suck (the flanges bend on 33's and 35's).
Not to mention, once you get an 8.8, you still have to build it. If you want a locker, shafts, and gears, you're looking at dumping another $2-2.5k into your 8.8 to get it to actually work how you want it to. The Super 35 does all of that for about $1.7k (price from my gear guy who is rather high with pricing: includes S35, ARB, and a regear to 4.88 for the rear, doesn't include front axle pricing), and you end up with an axle good enough for 35's with no fabrication required.
It's a bit of a no brainer to me. The other benefits are that you can build in stages rather than have to save up for everything and do it all at once. Both are good axles, the 35 will most likely be cheaper to get it set up with the same gears, lockers, and general capability.