I think the whole number of lugs in what circle thing boils down to a choice between integrating axles (it's easier to not have to change the bolt pattern on one or both axles) and trail swapping. I have waggy axles with 6 bolt wheels. Do I notice any difference between the 6 bolts and 5 on 4.5 I had before? No, other than I had to buy new wheels, and if I had a flat on the trail (and my spare was flat also) I can't borrow a tire from another jeep because it will likely have the wrong bolt pattern.
I believe the 8.8 DOES have the same bolt pattern as a stock jeep (5 on 4.5), and if it were me and I had to change one of those axles I'd change the 6 bolt to 5 on 4.5 just because on the trail I'd have more people I could 'borrow' from in an emergency..... but I don't know what's involved in change the 6 bolt to 5 on 4.5, or if it's even possible.
With stock gearing, you won't be 'screwed' but you will notice 5th gear is all but useless on the highway. My advice: go for the 35s. If you get smaller tires for the gearing, you will just end up selling them for bigger tires later on.
Keep in mind that you will almost certainly have to get new wheels anyway, even if the bolt pattern remains the same because stock wheels are not wide enough and have so much backspacing that with much wider tires you'll have too much interference and no turning radius. Go for cheap black steel - cheap, and no crying involved really when they get battle scarred, and they will.
Do you have the axles yet? If not, you might want to consider going D44 front and rear from a wagoneer or scout so that they both have the same bolt pattern. I know the 8.8 is somewhat stronger and has disk brakes, but ..... just a thought. Axle swaps seem a lot easier when you aren't trying to integrate different axle sets.