Ii was not party to the JQ 787 order process, but I have ordered a fleet of 36 new airliners once. Before the contract was signed every single option, provision for option, alternative vendor etc was hashed out. Sometimes from 08:00 tiil last drinks. Many times, in fact.
It isn't rocket surgery, but you have to pay attention. Having a couple of experienced pilots on the team is key. Eventually the winnowing should yield a useable compromise between the wish list and the essentials. Adequate thrust options rank higher than avionics suites. (Which are next on the list) Dispatch reliability is foremost: can you go? Can you go with a paying load? Can you go on time? 99.9% of the time? Why not?
The A330 initial order was screwed up, as was the follow-up domestic aircraft without brake fans. The 737-800 low thrust model, the 717 low thrust model are both examples of naive aircraft ordering. We have form in this department.
Manufacturers may sometimes offer guidance, but it is more fun for them to watch someone order a cripple: that way you get to sell the same customer twice for no extra effort. The guys who order the follow-on planes will not be the the guys from the first order, so no embarrassment to share.
Ordering planes is like contracting the building of a house: every change once the contract is signed is going to be costly...there are no free do-overs. It pays to do your homework before you accept that lunch date with the salesmen.
I am, however, standing by for the next round of cost-cuttiing, aware as I am that my pay is too generous and may compromise the long-term health of the company. Or something.