It seems like you are trading up parts to the same frame (maybe just a little newer and a different color) so depending on the trade in value you may be getting a good deal, but it may not using your available assets in the best way to achieve an increase in ride quality or speed if that is what you are after. The bike with the upgraded parts may function slightly smoother but I don't have experience with those two groups. The bike will not go any faster (although it will be a little lighter) and will likely not feel much different on the road (on the same frame the main ride quality difference will come from the wheels and tires tires but the two bikes have the same).
Personally in an upgrade, unless there was an aesthetic improvement I was after (which is an entirely valid reason to upgrade), I would be looking for a functional upgrade in either speed or comfort, or useability. Your consideration does add a couple gears and I like more gears.
I would personally go for wheels and tires. Those could add speed AND comfort. Barring that a quality set of tires is the easiest way to greatly change how a bike feels and behave on the road. And if one wanted speed, free speed, I would go with latex inner tubes. Save about 15-20 watts over regular butyl tubes which translates into about 1-1.5mph increase for the same riding effort. Of course you can throw new tires and tubes on any bike, even the new bike.
I'm curious what you'd get for a trade-in. No bike shops in my area do that.