On your list I'd go with the larger fuel tank and diesel. None of the other stuff interests me, I simply don't care. Toyota has never offered a 4:1 t-case and honestly I had a 4.7:1 Marlin that I replaced with a stock gearing because having those ratios is useful, at least more useful I find that not having them. The uber low gearing is only useful for crawling but I use my truck in other ways. And my truck has a 22R-E, so the low gearing is actually quite useful in the rocks. A 1GR has the power to deal with higher gearing.
Stuff like electrical sway bars, electric seats, electric rear window are things I /really/ do NOT want in my truck. I am weighing replacing my '91 with a new(er) Taco and it already irritates me that I'd be stuck with power windows, that stupid key fob thing, back up cameras and all that. I want something that's going to be with me 20+ years like my old truck and I figure all that crap is going to fail me long before the 1GR and the rest of the proven drivetrain.
I am not even that worried about a C-channel frame, but I do know the 1st gen Taco frame could fail so I'm of the opinion that a full box frame would be nice. But I thought Toyota beefed up the 2nd gen Taco frame, which is really the point. An open channel doesn't have to be weak, i.e. semi trucks, and can have the advantage of being able to be cleaned out to prevent rust. So in my mind it's not an absolute.
Vinyl floor, white, manual stuff. That's what I want.