Nav / I-Drive can't be retrofitted like the Golf, but I didn't opt for it due to me being already well over budget and it was another 2k. TBH, i've managed fine without it and the trusty Tom Tom comes out if I am lost. Does finish the dash off nicely though.
Leather is another popular option, but the car does come with the same seats in a half leather style material as stock.
For me, the must have was DCT, Xenons and Bluetooth (which in turn upgrades the stereo). Xenons (like the Golf) transform the front end of the car IMO. Plus I could never go back to standard headlights after having them. But like most options on most cars, it comes down to personal preference..
Regarding the N55 vs N54.. They both mod very much the same when mapping and adding things like DPs. But if you are wanting to go bonkers and add Meth etc, then the N54 is the way to go (at the min). N55 is slightly more efficient and does have a slightly better exhaust note. But to be honest, neither of them is IMO 'better' than the other.
If you want DCT (DSG) then you are limited to the N55. The N54 is available with the Steptronic Auto or MT.