StephenH

My thoughts:
9 speed/10 speed/11 speed- zero difference in riding and usability- but check at your bike shop as to parts availability on the different components. I think my shop upgraded my older bike from 9 to 10 speed because some of the 9-speed stuff wasn't available.
The Big Handlebar Bag (edited) Issue- considered essential by a lot of users, but hardly anyone around here uses one, and nobody seems the worse off for it, either.
Moving parts- I'd go with the higher-end in terms of quality, not necessarily weight. Your bottom bracket WILL go out sometime, somewhere, so the longer you can stave that off, the less likely to DNF on a ride.
Big tires- I use them for gravel rides, use 28's for everything else- don't go bigger unless you have specific reason to do so.
If there's a lot of parts where you just don't know the difference, buy a ready-built-up bike, otherwise, you're paying extra to have exactly the part you don't care about used there.
Generator hubs are great because you always have lights ready. I used to use battery systems, and I'd come in from a ride and forget to charge it for next time.