I highly recommend maple neck and maple fingerboard ...oh. Well chosen! I think the default is that it comes with a satin finish. I hope you're alright with that. I actually called my dealer back and made sure that was the case, because satin finish is best finish.
The other main thing is the pickups. I kind of dig covered pups, but if you want a tad more gain, you could opt for the 85/15 pups. I think the order of increasing gain after that goes: the 57/08, 59/09, the HFS/VB combination, and the \m/ pups. But I'm getting old and forgetful, so someone please double-check my work.
The other choices are hardware (nickel, gold, or hybrid) and colour. I personally think hybrid looks snappy as...
Obviously the best colour is Black Gold Burst, but we can't have an all black gold burst collection of guitars, so perhaps you could pick one of the more esoteric colours like Loch Ness Monster Green, Malaysian Pale Blue, or Cat's Tongue Pink. Note that some of the colours can have a natural back as an option. (My next guitar will be Bonnie Pink with a natural back, and maple neck and fretboard.)
In terms of prices, I don't know what any of those choices do to the price, you may want to run them by your dealer. In my case, I just ordered what I wanted and the dealer gave me a final best price that I was happy with, so I didn't have to cut any corners.
One of the choices that will definitely raise the price is getting a fancier case. I don't think that's even an option -- your dealer would have to buy the case and tack the case price on.