STRONG wheels, and 35-40mm tires, capable of 125-140 PSI.
V-Brakes are fine with me - llight and work very well.
OEM, read color matched, fenders (at least as an option.)
9 spd, minimum - with a 30-40-50 chainrings.
Lots of adjustability for seat posts, seat, bars, etc.
More integrated racks, and mount points. Both front, and rear.
More "water bottle type" mount points for everything from pumps to more water bottles (is 3 really enough for a LONG ride?).
More flat, straight, sections on bars for mounting stuff.
Aluminum frames are fine with me, even though there are some real lightweight steel frames available.
Handlebar lockout controls, on bikes with suspensions. For quick and easy changes. And, while there - easily maintainable and rebuildable front suspensions - you really should replace that oil, and put gaitors on the sliders to keep 'em cleaner.
GOOD, performance, flat resistant tires, like Schwalbe Marathon Supremes as OEM.
Integrated kickstand mounts (and, while you are at it - good seatstay and chainstay bridges for mounting fenders) with WIDE stays for any tires.
Pedals with zerks, for regreasing . Should make em last forever.
Better chains, with real "bushings" to cut down on wear. Chains today, are a real joke!
Any bicycle suspension (front, rear, seat, etc) should be able to be totally locked out.
You asked!