Well, I lucked out and found what amounts to the truck I would have ordered on a lot in Midtown Houston (go figure)...
But, my advice:
If you get a 4x4, get the steps. I never realized how much I used them on my last truck (they were just there) and I've had lifted 4x4's over the years. This one sits high enough (and those lifted trucks were 20+ years ago) that the step is worth it.
If you add electrical gear or lights to your trucks, the upfitter switches are a big win
I wish my truck came with the cab marker lights, but I bought them aftermarket and will install them myself...not a huge deal.
I think I'd like to have had the air-adjust suspension system, but I've never had one, so I can't miss it.
All other things being equal, I'd rather have a box camera than not...but mine didn't come with it, and I've never had one, so not a show-stopper.
Bedliner: Just do it. If you can get the factory spray-on bedliner, do it, if not, spray on a linex. You won't regret it. It should be about the same money either way.
If you're going to tow a gooseneck or 5th wheel, get the factory setup. If you're going to tow a gooseneck constantly (like in hotshot service) I'd seriously consider NOT getting the factory setup, and going with a B&W turnover hitch -- I prefer a gooseneck ball just forward of the rear axle, and the factory kit puts it dead center (to my eye) over the axle. This is a personal preference unless you are going to run 35K GVW all the time.
All that said, I'm probably not the right guy to ask...I prefer my trucks pretty plain as options go...I didn't want the 8.4 radio (too many touchy feely fiddly bits for me, too many subscriptions to keep up), I didn't want the dual-zone A/C, I didn't want carpet, I didn't want leather, etc. etc....what I wanted was what most dealers call a "fleet truck." I also tend to keep trucks 10+ years...if I traded every couple of years, I'd go for more goodies.