Some of these choices simply come down to what best suits you and your family, whereas others, like not ordering the table because you can get it aftermarket for less, are just common sense.
As you know, I just ordered a 28DSBH, with almost identical options. I didn't order 30lb tanks because they add a total of 30 lbs of tongue weight and they're less easily refilled. Plus, we don't plan to do tons of dry camping until our daughter is a little older. You can always carry another 20lb tank internally during transit and have the same standby capacity without adding tongue weight. If you don't order 30s you will get 20s with cover included.
I DID order the two electric stabilizer jacks rather than the four manual jacks, not because they're electric but because they're a tandem rather than independent setup, (supposedly) making for improved stability. Much like an aftermarket cross-brace stabilizer system, both legs adjust to the terrain and one another automatically, ensuring there's equal terrain pressure on each leg. If they fail, there's a manual option, and I'm not afraid to replace a motor down the road if need be. I'll post on how they work (or don't!) after our first trip in the new trailer this summer.
I didn't order the free-standing table and chairs because we have a toddler and the dinette works better for us, provides storage, and I don't have to strap down chairs during transit. I didn't order the bumper mount grill because they're largely crap and I plan to set up my outdoor kitchen near the front storage compartment. In that compartment, I plan to have an aftermarket fridge (Midea WHS-65SLB1, 1.6 cf, $91 on Amazon) because Jayco's is needlessly expensive and, by some accounts, very noisy up in the bedroom.
I did order the 5-way power remote (dealer gave it to me for $220), again because of the toddler, plus I like remotes and it will operate the power stabilizer jacks. I figure that if we get to a site after a long day on the road and my little one is fussy, mama may have to take care of her while dad drops the jacks, extends the slide and awning, etc. I think it's useful to be able to stand outside the trailer and watch the slide come out, so I won't have to guess about hitting nearby branches, etc. Anything that speeds setup on a July day with a two-year-old in attendance is a must have for me.
Like apr1967 and need-a-vacation, we were of mixed minds on the skylight. DW wanted it, but I thought about it as another roof hole/potential point of failure. And it can introduce a lot of heat to the inside on a summer day. But we ended up ordering it. I think now that the slide out has two side windows, the skylight is probably unnecessary, but it's a nice touch.
Last, on the EZBreeze, I figured I'd try taking the camper out as is and see how we do as equipped. I'm seeing the EZBreeze out there for $75-$100 and could always self install later, although if I put one in it will probably be a Fantastic fan with thermostat and rain sensor...
That's about it, I guess. Whatever you decide, the options you've selected already are going to make it one beautiful and comfortable TT!