Different ways of doing this stuff. Bugs are few until somewhere into the Sierras, so I liked carrying a poncho tarp as shelter and raingear for the first 700 miles, almost never set it up. Then swap to something that can create a bug-free-zone at Kennedy Meadows.
I did swap sleeping bags, used a 20F bag until done with the Sierras, used a 32F bag for the rest, but finished the trail before it was too-o cold for a 32F bag in northern WA.
You do want a pack strong/solid enough to carry more water than you might be used to in the first 700 miles. Not all the time, certainly, but you need to be able to do it.
The bigger "is my pack beefy enough" issue for me, however, was in the Sierras --- bear can, ice axe, maybe an extra clothing item or two and possibly microspikes depending on the year --- but also a long distance between resupply.
Tent stakes: take what you like. You won't be sleeping on sand (it's not like a 'Lawrence of Arabia' movie scene). In the cases where there's any problem you'll get good at using rocks or local sticks or something. It's not always easy on the AT either --- I recall a couple of times getting creative using those $#%^! tent platforms with my non-freestanding tent.
"Another thing is inflatables, will they last through the desert?"
I used an inflatable on all of the big 3 trails, to include through both SoCal and New Mexico (which latter had IMO a lot more "needles and stuff"). If you're concerned, consider bringing a 1/8" ccf pad and put it under your inflatable whenever sharp stuff is of a concern, and on top of it when you want a bit more warmth. Gossamer Gear sells one, I think there are other options listed elsewhere on this site.
It's possible that by the end of a thru-hike you'll have a slow leak. One of my pads I just know that in the middle of the night I'll have to reinflate; leak is too slow to find in the bathtub, just due to a lot of use I guess. Another is somewhat delaminated so that it bulges in a slightly uncomfortable way. At least with neo-air pads, I wouldn't expect to get a lot more than one thru-hike out of it, but you might do.
I've also seen the recommendation to avoid water bladders in "the desert" because of the needles. I can only speculate that folks are perhaps carrying them in external side mesh or not taking care when they throw them down on the ground or something as I've used bladders throughout (platypus) with never a leak.